7PKQ | pdb_00007pkq

Small subunit of the Chlamydomonas reinhardtii mitoribosome

PDB DOI: https://doi.org/10.2210/pdb7PKQ/pdb
EM Map EMD-13477: EMDB EMDataResource
NAKB: 7PKQ

Classification: RIBOSOME
Organism(s): Chlamydomonas reinhardtii
Mutation(s): No

Deposited: 2021-08-26 Released: 2023-06-14
Deposition Author(s): Waltz, F., Soufari, H., Hashem, Y.
Funding Organization(s): European Research Council (ERC), Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments

Waltz, F., Salinas-Giege, T., Englmeier, R., Meichel, H., Soufari, H., Kuhn, L., Pfeffer, S., Foerster, F., Engel, B.D., Giege, P., Drouard, L., Hashem, Y.

To be published.

Macromolecule Content

Total Structure Weight: 1,608.54 kDa
Atom Count: 70,313
Modeled Residue Count: 7,804
Deposited Residue Count: 13,373
Unique protein chains: 38
Unique nucleic acid chains: 4

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mS35	A [auth B]	883	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CST5 (Chlamydomonas reinhardtii) Explore A0A2K3CST5 Go to UniProtKB: A0A2K3CST5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K3CST5
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mS45	B [auth C]	999	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DM91 (Chlamydomonas reinhardtii) Explore A0A2K3DM91 Go to UniProtKB: A0A2K3DM91
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K3DM91
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mS45-insert	C [auth D]	425	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
mS31/46	D [auth K]	186	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
mS105	E [auth L], F [auth M], G [auth N]	271	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DAY3 (Chlamydomonas reinhardtii) Explore A0A2K3DAY3 Go to UniProtKB: A0A2K3DAY3
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UniProt Group	A0A2K3DAY3
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
mS106	H [auth O]	516	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DZV7 (Chlamydomonas reinhardtii) Explore A0A2K3DZV7 Go to UniProtKB: A0A2K3DZV7
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UniProt Group	A0A2K3DZV7
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
mS107	I [auth P]	416	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CRX4 (Chlamydomonas reinhardtii) Explore A0A2K3CRX4 Go to UniProtKB: A0A2K3CRX4
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UniProt Group	A0A2K3CRX4
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk1	J [auth U]	33	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk2	K [auth V]	152	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk3	L [auth W]	54	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk4	M [auth X]	81	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk5	N [auth Y]	108	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Unk6	O [auth Z]	571	Chlamydomonas reinhardtii	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
uS4m	P [auth d]	415	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3E198 (Chlamydomonas reinhardtii) Explore A0A2K3E198 Go to UniProtKB: A0A2K3E198
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UniProt Group	A0A2K3E198
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ribosomal protein S6	Q [auth f]	122	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8JGX6 (Chlamydomonas reinhardtii) Explore A8JGX6 Go to UniProtKB: A8JGX6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8JGX6
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
bS16m	R [auth p]	88	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3D9S4 (Chlamydomonas reinhardtii) Explore A0A2K3D9S4 Go to UniProtKB: A0A2K3D9S4
Entity Groups
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UniProt Group	A0A2K3D9S4
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
bS18m	S [auth r]	356	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DDW6 (Chlamydomonas reinhardtii) Explore A0A2K3DDW6 Go to UniProtKB: A0A2K3DDW6
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K3DDW6
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
mS26	T [auth w]	193	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DGK2 (Chlamydomonas reinhardtii) Explore A0A2K3DGK2 Go to UniProtKB: A0A2K3DGK2
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UniProt Group	A0A2K3DGK2
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
bS1m	Y [auth a]	253	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8IB56 (Chlamydomonas reinhardtii) Explore A8IB56 Go to UniProtKB: A8IB56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8IB56
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
uS2m	Z [auth b]	530	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CXL0 (Chlamydomonas reinhardtii) Explore A0A2K3CXL0 Go to UniProtKB: A0A2K3CXL0
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UniProt Group	A0A2K3CXL0
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
S5 DRBM domain-containing protein	AA [auth e]	368	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DFB5 (Chlamydomonas reinhardtii) Explore A0A2K3DFB5 Go to UniProtKB: A0A2K3DFB5
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UniProt Group	A0A2K3DFB5
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
uS15m	BA [auth o]	319	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CQY8 (Chlamydomonas reinhardtii) Explore A0A2K3CQY8 Go to UniProtKB: A0A2K3CQY8
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UniProt Group	A0A2K3CQY8
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
mS34	CA [auth z]	133	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DPT3 (Chlamydomonas reinhardtii) Explore A0A2K3DPT3 Go to UniProtKB: A0A2K3DPT3
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UniProt Group	A0A2K3DPT3
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
mS23	DA [auth v]	190	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8IW03 (Chlamydomonas reinhardtii) Explore A8IW03 Go to UniProtKB: A8IW03
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UniProt Group	A8IW03
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
uS17m	EA [auth q]	220	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DKB4 (Chlamydomonas reinhardtii) Explore A0A2K3DKB4 Go to UniProtKB: A0A2K3DKB4
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UniProt Group	A0A2K3DKB4
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
uS12m	FA [auth l]	128	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3E3V0 (Chlamydomonas reinhardtii) Explore A0A2K3E3V0 Go to UniProtKB: A0A2K3E3V0
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UniProt Group	A0A2K3E3V0
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
uS8m	GA [auth h]	412	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CNM3 (Chlamydomonas reinhardtii) Explore A0A2K3CNM3 Go to UniProtKB: A0A2K3CNM3
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UniProt Group	A0A2K3CNM3
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
uS11m	HA [auth k]	233	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DQ48 (Chlamydomonas reinhardtii) Explore A0A2K3DQ48 Go to UniProtKB: A0A2K3DQ48
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UniProt Group	A0A2K3DQ48
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_S10 domain-containing protein	IA [auth j]	612	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CN25 (Chlamydomonas reinhardtii) Explore A0A2K3CN25 Go to UniProtKB: A0A2K3CN25
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UniProt Group	A0A2K3CN25
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ribosomal protein S13	JA [auth m]	124	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8J3J1 (Chlamydomonas reinhardtii) Explore A8J3J1 Go to UniProtKB: A8J3J1
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UniProt Group	A8J3J1
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial ribosomal protein S14	KA [auth n]	112	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8J6P9 (Chlamydomonas reinhardtii) Explore A8J6P9 Go to UniProtKB: A8J6P9
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UniProt Group	A8J6P9
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
Plastid-specific ribosomal protein 4	LA [auth u]	136	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8J1A6 (Chlamydomonas reinhardtii) Explore A8J1A6 Go to UniProtKB: A8J1A6
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UniProt Group	A8J1A6
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
uS19m	MA [auth s]	116	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DHN0 (Chlamydomonas reinhardtii) Explore A0A2K3DHN0 Go to UniProtKB: A0A2K3DHN0
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UniProt Group	A0A2K3DHN0
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
uS7m,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein,Ribosomal_S7 domain-containing protein	NA [auth g]	324	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3CXT8 (Chlamydomonas reinhardtii) Explore A0A2K3CXT8 Go to UniProtKB: A0A2K3CXT8
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UniProt Group	A0A2K3CXT8
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9, chloroplastic	OA [auth i]	446	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3E2Q3 (Chlamydomonas reinhardtii) Explore A0A2K3E2Q3 Go to UniProtKB: A0A2K3E2Q3
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UniProt Group	A0A2K3E2Q3
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
mS29	PA [auth x]	485	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3DXG4 (Chlamydomonas reinhardtii) Explore A0A2K3DXG4 Go to UniProtKB: A0A2K3DXG4
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UniProt Group	A0A2K3DXG4
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal_S3_C domain-containing protein	QA [auth c]	490	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A0A2K3D7R0 (Chlamydomonas reinhardtii) Explore A0A2K3D7R0 Go to UniProtKB: A0A2K3D7R0
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UniProt Group	A0A2K3D7R0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
mS33	RA [auth y]	209	Chlamydomonas reinhardtii	Mutation(s): 0
UniProt
Find proteins for A8JI15 (Chlamydomonas reinhardtii) Explore A8JI15 Go to UniProtKB: A8JI15
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A8JI15
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 19
S1 rRNA	U [auth 1]	101	Chlamydomonas reinhardtii
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Molecule	Chains	Length	Organism
Entity ID: 20
S4 rRNA	V [auth 4]	415	Chlamydomonas reinhardtii
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Molecule	Chains	Length	Organism
Entity ID: 21
S2 rRNA	W [auth 2]	213	Chlamydomonas reinhardtii
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Molecule	Chains	Length	Organism
Entity ID: 22
S3 rRNA	X [auth 3]	393	Chlamydomonas reinhardtii
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Waltz, F.

Soufari, H.

Hashem, Y.

Funding Organization	Location	Grant Number
European Research Council (ERC)	France	TransTryp ID:759120
Agence Nationale de la Recherche (ANR)	France	ANR-11-LABX-0057_MITOCROSS
Agence Nationale de la Recherche (ANR)	France	MITRA, ANR-16-CE11-0024-02
Agence Nationale de la Recherche (ANR)	France	DAMIA, ANR-20-CE11-0021

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2024-07-17
Changes: Data collection

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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.

7PKQ | pdb_00007pkq

Small subunit of the Chlamydomonas reinhardtii mitoribosome

Literature

The Chlamydomonas mitochondrial ribosome: how to build a ribosome from RNA fragments

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

Entity ID: 4

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

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Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

Entity ID: 9

Entity ID: 10

Entity ID: 11

Entity ID: 12

Entity ID: 13

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 23

UniProt

Entity Groups

Sequence Annotations

Entity ID: 24

UniProt

Entity Groups

Sequence Annotations

Entity ID: 25

UniProt

Entity Groups

Sequence Annotations

Entity ID: 26

UniProt

Entity Groups

Sequence Annotations

Entity ID: 27

UniProt

Entity Groups

Sequence Annotations

Entity ID: 28

UniProt

Entity Groups

Sequence Annotations

Entity ID: 29

UniProt