4V66 | pdb_00004v66

Structure of the E. coli ribosome and the tRNAs in Post-accommodation state

PDB DOI: https://doi.org/10.2210/pdb4V66/pdb
Entry: 4V66 supersedes: 3E1D, 3E1C
EM Map EMD-1056: EMDB EMDataResource
NAKB: 4V66

Classification: RIBOSOME
Organism(s): Escherichia coli, Sulfolobus acidocaldarius
Mutation(s): No

Deposited: 2008-08-03 Released: 2014-07-09
Deposition Author(s): Devkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 9.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading

Devkota, B., Caulfield, T.R., Tan, R.-Z., Harvey, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 2,242.45 kDa
Atom Count: 149,248
Modeled Residue Count: 10,740
Deposited Residue Count: 10,970
Unique protein chains: 50
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	F [auth AB]	241	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12)) Explore P0A7V0 Go to UniProtKB: P0A7V0
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V0
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	G [auth AC]	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9 Go to UniProtKB: P0A7R9
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UniProt Group	P0A7R9
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	H [auth AD]	124	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S3 (Escherichia coli (strain K12)) Explore P0A7S3 Go to UniProtKB: P0A7S3
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UniProt Group	P0A7S3
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	I [auth AF]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9 Go to UniProtKB: P0A7S9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7S9
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14	J [auth AG]	101	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG59 (Escherichia coli (strain K12)) Explore P0AG59 Go to UniProtKB: P0AG59
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AG59
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	K [auth AH]	89	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for Q8X9M2 (Escherichia coli O157:H7) Explore Q8X9M2 Go to UniProtKB: Q8X9M2
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8X9M2
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	L [auth AI]	82	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7T3 (Escherichia coli (strain K12)) Explore P0A7T3 Go to UniProtKB: P0A7T3
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UniProt Group	P0A7T3
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	M [auth AJ]	84	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12)) Explore P0AG63 Go to UniProtKB: P0AG63
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UniProt Group	P0AG63
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	N [auth AK]	75	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7 Go to UniProtKB: P0A7T7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7T7
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	O [auth AL]	92	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12)) Explore P0A7U3 Go to UniProtKB: P0A7U3
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UniProt Group	P0A7U3
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	P [auth AN]	87	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7 Go to UniProtKB: P0A7U7
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UniProt Group	P0A7U7
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	Q [auth AO]	233	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V3 (Escherichia coli (strain K12)) Explore P0A7V3 Go to UniProtKB: P0A7V3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V3
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S21	R [auth AQ]	71	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P68679 (Escherichia coli (strain K12)) Explore P68679 Go to UniProtKB: P68679
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68679
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	S [auth AR]	206	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7V8 (Escherichia coli (strain K12)) Explore P0A7V8 Go to UniProtKB: P0A7V8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7V8
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	T [auth AS]	159	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7W1 (Escherichia coli (strain K12)) Explore P0A7W1 Go to UniProtKB: P0A7W1
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7W1
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	U [auth AT]	135	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02358 (Escherichia coli (strain K12)) Explore P02358 Go to UniProtKB: P02358
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02358
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	V [auth AU]	179	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359 Go to UniProtKB: P02359
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02359
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	W [auth AV]	130	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for Q3YWV3 (Shigella sonnei (strain Ss046)) Explore Q3YWV3 Go to UniProtKB: Q3YWV3
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UniProt Group	Q3YWV3
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	X [auth AW]	130	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7X3 (Escherichia coli (strain K12)) Explore P0A7X3 Go to UniProtKB: P0A7X3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7X3
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	Y [auth AX]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R5 (Escherichia coli (strain K12)) Explore P0A7R5 Go to UniProtKB: P0A7R5
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UniProt Group	P0A7R5
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	BA [auth BC]	94	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P68919 (Escherichia coli (strain K12)) Explore P68919 Go to UniProtKB: P68919
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UniProt Group	P68919
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	CA [auth BD]	123	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12)) Explore P0ADY3 Go to UniProtKB: P0ADY3
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UniProt Group	P0ADY3
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	DA [auth BE]	144	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02413 (Escherichia coli (strain K12)) Explore P02413 Go to UniProtKB: P02413
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UniProt Group	P02413
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	EA [auth BF]	136	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADY7 (Escherichia coli (strain K12)) Explore P0ADY7 Go to UniProtKB: P0ADY7
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UniProt Group	P0ADY7
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	FA [auth BG]	127	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG44 (Escherichia coli (strain K12)) Explore P0AG44 Go to UniProtKB: P0AG44
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UniProt Group	P0AG44
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	GA [auth BH]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12)) Explore P0C018 Go to UniProtKB: P0C018
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UniProt Group	P0C018
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	HA [auth BI]	115	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
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UniProt Group	P0A7K6
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	IA [auth BJ]	118	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3 Go to UniProtKB: P0A7L3
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UniProt Group	P0A7L3
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	JA [auth BK]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12)) Explore P0AG48 Go to UniProtKB: P0AG48
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UniProt Group	P0AG48
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	KA [auth BL]	110	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
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UniProt Group	P61175
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	LA [auth BM]	99	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12)) Explore P0ADZ0 Go to UniProtKB: P0ADZ0
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UniProt Group	P0ADZ0
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	MA [auth BN]	270	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422 Go to UniProtKB: P60422
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UniProt Group	P60422
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	NA [auth BO]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60624 (Escherichia coli (strain K12)) Explore P60624 Go to UniProtKB: P60624
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UniProt Group	P60624
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	OA [auth BP]	85	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
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UniProt Group	P0A7L8
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	PA [auth BQ]	63	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12)) Explore P0A7M6 Go to UniProtKB: P0A7M6
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UniProt Group	P0A7M6
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	QA [auth BR]	59	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12)) Explore P0AG51 Go to UniProtKB: P0AG51
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UniProt Group	P0AG51
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	RA [auth BS]	70	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12)) Explore P0A7M9 Go to UniProtKB: P0A7M9
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UniProt Group	P0A7M9
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	SA [auth BT]	57	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4 Go to UniProtKB: P0A7N4
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UniProt Group	P0A7N4
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	TA [auth BU]	54	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12)) Explore P0A7N9 Go to UniProtKB: P0A7N9
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UniProt Group	P0A7N9
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	UA [auth BV]	46	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12)) Explore P0A7P5 Go to UniProtKB: P0A7P5
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UniProt Group	P0A7P5
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	VA [auth BW]	64	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12)) Explore P0A7Q1 Go to UniProtKB: P0A7Q1
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UniProt Group	P0A7Q1
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	WA [auth BX]	38	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12)) Explore P0A7Q6 Go to UniProtKB: P0A7Q6
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UniProt Group	P0A7Q6
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	XA [auth BY]	209	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60438 (Escherichia coli (strain K12)) Explore P60438 Go to UniProtKB: P60438
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UniProt Group	P60438
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1P	YA [auth BZ]	213	Sulfolobus acidocaldarius	Mutation(s): 0
UniProt
Find proteins for P35024 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)) Explore P35024 Go to UniProtKB: P35024
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UniProt Group	P35024
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	ZA [auth B1]	201	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60723 (Escherichia coli (strain K12)) Explore P60723 Go to UniProtKB: P60723
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UniProt Group	P60723
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	AB [auth B2]	178	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P62399 (Escherichia coli (strain K12)) Explore P62399 Go to UniProtKB: P62399
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UniProt Group	P62399
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	BB [auth B3]	177	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AG55 (Escherichia coli (strain K12)) Explore P0AG55 Go to UniProtKB: P0AG55
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UniProt Group	P0AG55
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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	CB [auth B4]	149	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12)) Explore P0A7R1 Go to UniProtKB: P0A7R1
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UniProt Group	P0A7R1
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	DB [auth B5]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7 Go to UniProtKB: P0A7J7
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UniProt Group	P0A7J7
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	EB [auth B6]	140	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
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UniProt Group	P0AA10
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
A/T, P and E-site tRNAs	A [auth AA], B [auth AP], C [auth AE]	76	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 2
mRNA model	D [auth AM]	20	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 3
16S rRNA	E [auth A1]	1,530	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 24
5S rRNA	Z [auth BA]	117	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 25
23S rRNA	AA [auth BB]	2,903	Escherichia coli
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 9.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

This entry supersedes: 3E1D, 3E1C

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2014-12-10
Changes: Other
Version 1.2: 2015-03-25
Changes: Other
Version 1.3: 2018-07-18
Changes: Data collection
Version 1.4: 2019-12-18
Changes: Database references, Other
Version 1.5: 2024-02-28
Changes: Data collection, Database references, Refinement description

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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.

4V66 | pdb_00004v66

Structure of the E. coli ribosome and the tRNAs in Post-accommodation state

Literature

The Structure of the E. coli Ribosome Before and After Accommodation: Implications for Proofreading

Biological Assembly 1

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