7QEP | pdb_00007qep

Cryo-EM structure of the ribosome from Encephalitozoon cuniculi

PDB DOI: https://doi.org/10.2210/pdb7QEP/pdb
NAKB: 7QEP
EM Map EMD-13936: EMDB EMDataResource

Classification: RIBOSOME
Organism(s): Encephalitozoon cuniculi GB-M1
Mutation(s): Yes

Deposited: 2021-12-03 Released: 2022-02-09
Deposition Author(s): Nicholson, D., Ranson, N.A., Melnikov, S.V.
Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom), H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Adaptation to genome decay in the structure of the smallest eukaryotic ribosome

Nicholson, D., Salamina, M., Panek, J., Helena-Bueno, K., Brown, C.R., Hirt, R.P., Ranson, N.A., Melnikov, S.V.

(2022) Nat Commun 13: 591

DOI: https://doi.org/10.1038/s41467-022-28281-0

Macromolecule Content

Total Structure Weight: 2,597.77 kDa
Atom Count: 166,112
Modeled Residue Count: 14,617
Deposited Residue Count: 15,601
Unique protein chains: 74
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide binding protein beta subunit	A [auth RA]	334	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for M1K775 (Encephalitozoon cuniculi) Explore M1K775 Go to UniProtKB: M1K775
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UniProt Group	M1K775
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S10	E [auth C0]	96	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS17 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS17 Go to UniProtKB: Q8SS17
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UniProt Group	Q8SS17
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S11	F [auth C1]	156	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS53 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS53 Go to UniProtKB: Q8SS53
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UniProt Group	Q8SS53
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S12	G [auth C2]	134	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSK9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSK9 Go to UniProtKB: Q8SSK9
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UniProt Group	Q8SSK9
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S13	H [auth C3]	148	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRB3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRB3 Go to UniProtKB: Q8SRB3
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UniProt Group	Q8SRB3
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S14	I [auth C4]	134	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSA6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSA6 Go to UniProtKB: Q8SSA6
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UniProt Group	Q8SSA6
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBOSOMAL PROTEIN S15	J [auth C5]	148	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRE7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRE7 Go to UniProtKB: Q8SRE7
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UniProt Group	Q8SRE7
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S16	K [auth C6]	145	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSC2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSC2 Go to UniProtKB: Q8SSC2
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UniProt Group	Q8SSC2
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S17	L [auth C7]	120	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSF9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSF9 Go to UniProtKB: Q8SSF9
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UniProt Group	Q8SSF9
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S18	M [auth C8]	153	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRP2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRP2 Go to UniProtKB: Q8SRP2
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UniProt Group	Q8SRP2
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S19	N [auth C9]	137	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQS8 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQS8 Go to UniProtKB: Q8SQS8
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UniProt Group	Q8SQS8
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S20	O [auth D0]	120	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQX6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQX6 Go to UniProtKB: Q8SQX6
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UniProt Group	Q8SQX6
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ECU11_0225 protein	P [auth D1]	70	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for I7L8M6 (Encephalitozoon cuniculi (strain GB-M1)) Explore I7L8M6 Go to UniProtKB: I7L8M6
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UniProt Group	I7L8M6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S15A (S22 in yeast)	Q [auth D2]	128	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQL9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQL9 Go to UniProtKB: Q8SQL9
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UniProt Group	Q8SQL9
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S23	R [auth D3]	140	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR65 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR65 Go to UniProtKB: Q8SR65
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UniProt Group	Q8SR65
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S24	S [auth D4]	131	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR06 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR06 Go to UniProtKB: Q8SR06
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UniProt Group	Q8SR06
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S25	T [auth D5]	109	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8STD9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8STD9 Go to UniProtKB: Q8STD9
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UniProt Group	Q8STD9
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S26	U [auth D6]	105	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRN2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRN2 Go to UniProtKB: Q8SRN2
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UniProt Group	Q8SRN2
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S27	V [auth D7]	85	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS34 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS34 Go to UniProtKB: Q8SS34
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UniProt Group	Q8SS34
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S28	W [auth D8]	65	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQM2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQM2 Go to UniProtKB: Q8SQM2
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UniProt Group	Q8SQM2
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S29	X [auth D9]	66	Encephalitozoon cuniculi GB-M1	Mutation(s): 0

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Similarity to monoubiquitin/carboxy-extension protein fusion	Y [auth E1]	152	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SWB3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SWB3 Go to UniProtKB: Q8SWB3
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UniProt Group	Q8SWB3
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L1	Z [auth L1]	219	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRY5 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRY5 Go to UniProtKB: Q8SRY5
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UniProt Group	Q8SRY5
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8	AA [auth L2]	239	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSM6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSM6 Go to UniProtKB: Q8SSM6
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UniProt Group	Q8SSM6
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	BA [auth L3]	383	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQI3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQI3 Go to UniProtKB: Q8SQI3
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UniProt Group	Q8SQI3
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L4	CA [auth L4]	335	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRC2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRC2 Go to UniProtKB: Q8SRC2
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UniProt Group	Q8SRC2
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L5	DA [auth L5]	287	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRQ3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRQ3 Go to UniProtKB: Q8SRQ3
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UniProt Group	Q8SRQ3
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L6	EA [auth L6]	171	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR91 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR91 Go to UniProtKB: Q8SR91
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UniProt Group	Q8SR91
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7	FA [auth L7]	239	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS93 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS93 Go to UniProtKB: Q8SS93
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UniProt Group	Q8SS93
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7a	GA [auth L8]	206	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSG1 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSG1 Go to UniProtKB: Q8SSG1
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UniProt Group	Q8SSG1
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L9	HA [auth L9]	183	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSF7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSF7 Go to UniProtKB: Q8SSF7
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UniProt Group	Q8SSF7
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	IA [auth M0]	219	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR96 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR96 Go to UniProtKB: Q8SR96
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UniProt Group	Q8SR96
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11	JA [auth M1]	173	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSG9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSG9 Go to UniProtKB: Q8SSG9
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UniProt Group	Q8SSG9
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L13	KA [auth M3]	163	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSC1 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSC1 Go to UniProtKB: Q8SSC1
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UniProt Group	Q8SSC1
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
ECU06_1215 protein	LA [auth M4]	106	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for I7L8J2 (Encephalitozoon cuniculi (strain GB-M1)) Explore I7L8J2 Go to UniProtKB: I7L8J2
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UniProt Group	I7L8J2
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L15	MA [auth M5]	204	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQU2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQU2 Go to UniProtKB: Q8SQU2
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UniProt Group	Q8SQU2
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L13A (L16)	NA [auth M6]	198	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS16 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS16 Go to UniProtKB: Q8SS16
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UniProt Group	Q8SS16
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L17	OA [auth M7]	183	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRH7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRH7 Go to UniProtKB: Q8SRH7
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UniProt Group	Q8SRH7
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L18	PA [auth M8]	200	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS76 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS76 Go to UniProtKB: Q8SS76
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UniProt Group	Q8SS76
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L19	QA [auth M9]	171	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRP5 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRP5 Go to UniProtKB: Q8SRP5
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UniProt Group	Q8SRP5
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein ECU01_0250	RA [auth MD]	171	Encephalitozoon cuniculi GB-M1	Mutation(s): 1
UniProt
Find proteins for Q8SWQ4 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SWQ4 Go to UniProtKB: Q8SWQ4
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UniProt Group	Q8SWQ4
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
ECU06_1135 protein	SA [auth MS]	73	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for I7IV41 (Encephalitozoon cuniculi (strain GB-M1)) Explore I7IV41 Go to UniProtKB: I7IV41
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UniProt Group	I7IV41
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L20	TA [auth N0]	188	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRD7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRD7 Go to UniProtKB: Q8SRD7
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UniProt Group	Q8SRD7
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21	UA [auth N1]	160	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRW8 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRW8 Go to UniProtKB: Q8SRW8
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UniProt Group	Q8SRW8
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22	VA [auth N2]	112	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS49 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS49 Go to UniProtKB: Q8SS49
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UniProt Group	Q8SS49
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23	WA [auth N3]	146	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRA7 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRA7 Go to UniProtKB: Q8SRA7
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UniProt Group	Q8SRA7
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
Similarity to 60S RIBOSOMAL PROTEIN L24	XA [auth N4]	100	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SUZ9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SUZ9 Go to UniProtKB: Q8SUZ9
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UniProt Group	Q8SUZ9
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L23A	YA [auth N5]	105	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR87 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR87 Go to UniProtKB: Q8SR87
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UniProt Group	Q8SR87
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L26	ZA [auth N6]	143	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRE6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRE6 Go to UniProtKB: Q8SRE6
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UniProt Group	Q8SRE6
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L27	AB [auth N7]	126	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS64 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS64 Go to UniProtKB: Q8SS64
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UniProt Group	Q8SS64
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27a	BB [auth N8]	147	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for O62581 (Encephalitozoon cuniculi (strain GB-M1)) Explore O62581 Go to UniProtKB: O62581
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UniProt Group	O62581
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	CB [auth N9]	57	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for I7JTZ6 (Encephalitozoon cuniculi (strain GB-M1)) Explore I7JTZ6 Go to UniProtKB: I7JTZ6
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UniProt Group	I7JTZ6
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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L30	DB [auth O0]	108	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRU1 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRU1 Go to UniProtKB: Q8SRU1
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UniProt Group	Q8SRU1
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31	EB [auth O1]	111	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSC8 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSC8 Go to UniProtKB: Q8SSC8
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UniProt Group	Q8SSC8
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	FB [auth O2]	139	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS18 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS18 Go to UniProtKB: Q8SS18
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UniProt Group	Q8SS18
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Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L35A (L33)	GB [auth O3]	113	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSF3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSF3 Go to UniProtKB: Q8SSF3
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UniProt Group	Q8SSF3
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Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34	HB [auth O4]	110	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SSA2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SSA2 Go to UniProtKB: Q8SSA2
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UniProt Group	Q8SSA2
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Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-1	IB [auth O5]	122	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8ST62 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8ST62 Go to UniProtKB: Q8ST62
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UniProt Group	Q8ST62
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Entity ID: 62
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36	JB [auth O6]	94	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRP1 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRP1 Go to UniProtKB: Q8SRP1
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UniProt Group	Q8SRP1
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Entity ID: 63
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37	KB [auth O7]	90	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRH5 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRH5 Go to UniProtKB: Q8SRH5
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UniProt Group	Q8SRH5
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Entity ID: 64
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	LB [auth O9]	52	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQP8 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQP8 Go to UniProtKB: Q8SQP8
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UniProt Group	Q8SQP8
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Entity ID: 65
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION	MB [auth P0]	131	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRH8 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRH8 Go to UniProtKB: Q8SRH8
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UniProt Group	Q8SRH8
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Entity ID: 66
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L44	NB [auth P2]	104	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SR18 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SR18 Go to UniProtKB: Q8SR18
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UniProt Group	Q8SR18
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Entity ID: 67
Molecule	Chains	Sequence Length	Organism	Details	Image
60S RIBOSOMAL PROTEIN L37A (L43)	OB [auth P3]	89	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRJ2 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRJ2 Go to UniProtKB: Q8SRJ2
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UniProt Group	Q8SRJ2
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Entity ID: 68
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S0	PB [auth S0]	252	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS60 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS60 Go to UniProtKB: Q8SS60
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UniProt Group	Q8SS60
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Entity ID: 69
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S1	QB [auth S1]	239	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS05 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS05 Go to UniProtKB: Q8SS05
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UniProt Group	Q8SS05
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Entity ID: 70
Molecule	Chains	Sequence Length	Organism	Details	Image
40S RIBOSOMAL PROTEIN S2	RB [auth S2]	242	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRG6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRG6 Go to UniProtKB: Q8SRG6
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UniProt Group	Q8SRG6
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Entity ID: 71
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S3	SB [auth S3]	216	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQM3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQM3 Go to UniProtKB: Q8SQM3
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UniProt Group	Q8SQM3
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Entity ID: 72
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S4	TB [auth S4]	268	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRB9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRB9 Go to UniProtKB: Q8SRB9
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UniProt Group	Q8SRB9
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Entity ID: 73
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S5	UB [auth S5]	189	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SS72 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SS72 Go to UniProtKB: Q8SS72
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UniProt Group	Q8SS72
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Entity ID: 74
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S6	VB [auth S6]	217	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRY0 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRY0 Go to UniProtKB: Q8SRY0
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UniProt Group	Q8SRY0
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Entity ID: 75
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S7	WB [auth S7]	170	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SQX3 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SQX3 Go to UniProtKB: Q8SQX3
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UniProt Group	Q8SQX3
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Entity ID: 76
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S8	XB [auth S8]	173	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SWC9 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SWC9 Go to UniProtKB: Q8SWC9
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UniProt Group	Q8SWC9
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Entity ID: 77
Molecule	Chains	Sequence Length	Organism	Details	Image
40S ribosomal protein S9	YB [auth S9]	184	Encephalitozoon cuniculi GB-M1	Mutation(s): 0
UniProt
Find proteins for Q8SRW6 (Encephalitozoon cuniculi (strain GB-M1)) Explore Q8SRW6 Go to UniProtKB: Q8SRW6
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UniProt Group	Q8SRW6
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
5.8S-23S ribosomal RNA	B [auth 1]	2,486	Encephalitozoon cuniculi GB-M1
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Molecule	Chains	Length	Organism
Entity ID: 3
5S ribosomal RNA	C [auth 2]	119	Encephalitozoon cuniculi GB-M1
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Molecule	Chains	Length	Organism
Entity ID: 4
18S ribosomal RNA	D [auth 3]	1,300	Encephalitozoon cuniculi GB-M1
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download:Ideal Coordinates CCD File SDF format, chain DC [auth L9] MOL2 format, chain DC [auth L9] mmCIF format, chain DC [auth L9]	DC [auth L9]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain DC [auth L9] Interactions & Density Focus chain DC [auth L9]
SPD Query on SPD Download:Ideal Coordinates CCD File SDF format, chain EC [auth N8] MOL2 format, chain EC [auth N8] mmCIF format, chain EC [auth N8]	EC [auth N8]	SPERMIDINE C₇ H₁₉ N₃ ATHGHQPFGPMSJY-UHFFFAOYSA-N		Interactions Focus chain EC [auth N8] Interactions & Density Focus chain EC [auth N8]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZB [auth D6] SDF format, chain IC [auth P3] SDF format, chain HC [auth P2] SDF format, chain GC [auth P0] SDF format, chain FC [auth O7] SDF format, chain CC [auth E1] SDF format, chain BC [auth D9] SDF format, chain AC [auth D7] MOL2 format, chain ZB [auth D6] MOL2 format, chain IC [auth P3] MOL2 format, chain HC [auth P2] MOL2 format, chain GC [auth P0] MOL2 format, chain FC [auth O7] MOL2 format, chain CC [auth E1] MOL2 format, chain BC [auth D9] MOL2 format, chain AC [auth D7] mmCIF format, chain ZB [auth D6] mmCIF format, chain IC [auth P3] mmCIF format, chain HC [auth P2] mmCIF format, chain GC [auth P0] mmCIF format, chain FC [auth O7] mmCIF format, chain CC [auth E1] mmCIF format, chain BC [auth D9] mmCIF format, chain AC [auth D7]	AC [auth D7] BC [auth D9] CC [auth E1] FC [auth O7] GC [auth P0] AC [auth D7], BC [auth D9], CC [auth E1], FC [auth O7], GC [auth P0], HC [auth P2], IC [auth P3], ZB [auth D6]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AC [auth D7] Focus chain BC [auth D9] Focus chain CC [auth E1] Focus chain FC [auth O7] Focus chain GC [auth P0] Focus chain HC [auth P2] Focus chain IC [auth P3] Focus chain ZB [auth D6] Interactions & Density Focus chain AC [auth D7] Focus chain BC [auth D9] Focus chain CC [auth E1] Focus chain FC [auth O7] Focus chain GC [auth P0] Focus chain HC [auth P2] Focus chain IC [auth P3] Focus chain ZB [auth D6]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.14

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Nicholson, D.

Ranson, N.A.

Melnikov, S.V.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	203743/Z/16/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	G0901526
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/N009738/1
H2020 Marie Curie Actions of the European Commission	United Kingdom	97617
H2020 Marie Curie Actions of the European Commission	United Kingdom	895166
Wellcome Trust	United Kingdom	108466/Z/15/Z

Revision History (Full details and data files)

Version 1.0: 2022-02-09
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Refinement description, Structure summary

RCSB PDB is hosted by

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Nucleic Acid Knowledgebase

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7QEP | pdb_00007qep

Cryo-EM structure of the ribosome from Encephalitozoon cuniculi

Literature

Adaptation to genome decay in the structure of the smallest eukaryotic ribosome

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

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Entity ID: 5

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Entity ID: 10

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Entity ID: 12

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Entity ID: 13

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Entity ID: 16

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Entity ID: 20

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Entity ID: 21

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Entity ID: 22

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