4V47 | pdb_00004v47

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome

PDB DOI: https://doi.org/10.2210/pdb4V47/pdb
Entry: 4V47 supersedes: 1P85, 1P6G
NAKB: 4V47

Classification: RIBOSOME
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 2003-05-06 Released: 2014-07-09
Deposition Author(s): Gao, H., Sengupta, J., Valle, M., Korostelev, A., Eswar, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.T., Sali, A., Chapman, M.S., Frank, J.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 12.3 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

Study of the structural dynamics of the E. coli 70S ribosome using real space refinement

Gao, H., Sengupta, J., Valle, M., Korostelev, A., Eswar, N., Stagg, S.M., Van Roey, P., Agrawal, R.K., Harvey, S.T., Sali, A., Chapman, M.S., Frank, J.

(2003) Cell 113: 789-801

PubMed: 12809609 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(03)00427-6
Primary Citation Related Structures:
4V47, 4V48

PubMed Abstract:
Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.

Organizational Affiliation

Howard Hughes Medical Institute, Health Research, Inc, Empire State Plaza, Albany, NY 12201, USA.

Macromolecule Content

Total Structure Weight: 2,075.02 kDa
Atom Count: 8,647
Modeled Residue Count: 8,647
Deposited Residue Count: 9,921
Unique protein chains: 43
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	C [auth AA]	272	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P60422 (Escherichia coli (strain K12)) Explore P60422 Go to UniProtKB: P60422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60422
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	D [auth AB]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60438
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	E [auth AC]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60723
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	F [auth AD]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62399
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	G [auth AE]	176	Escherichia coli	Mutation(s): 0

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L9	H [auth AF]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R1
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	I [auth AG]	141	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7J7 (Escherichia coli (strain K12)) Explore P0A7J7 Go to UniProtKB: P0A7J7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7J7
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	J [auth AH]	142	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12)) Explore P0AA10 Go to UniProtKB: P0AA10
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AA10
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	K [auth AI]	123	Escherichia coli	Mutation(s): 0

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	L [auth AJ]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02413
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	M [auth AK]	136	Escherichia coli	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	N [auth AL]	127	Escherichia coli	Mutation(s): 0

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	O [auth AM]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C018
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	P [auth AN]	114	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12)) Explore P0A7K6 Go to UniProtKB: P0A7K6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7K6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	Q [auth AO]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L3 (Escherichia coli (strain K12)) Explore P0A7L3 Go to UniProtKB: P0A7L3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7L3
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	R [auth AQ]	110	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P61175 (Escherichia coli (strain K12)) Explore P61175 Go to UniProtKB: P61175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61175
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	S [auth AR]	100	Escherichia coli	Mutation(s): 0

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	T [auth AS]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60624
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	U [auth AT]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68919
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	V [auth AU]	84	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12)) Explore P0A7L8 Go to UniProtKB: P0A7L8
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7L8
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	W [auth AW]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7M6
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	X [auth AX]	58	Escherichia coli	Mutation(s): 0

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	Y [auth AZ]	56	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12)) Explore P0A7N4 Go to UniProtKB: P0A7N4
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7N4
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	Z [auth A1]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7N9
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	AA [auth A4]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7Q6
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	CA [auth BC]	232	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: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	DA [auth BD]	205	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: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	EA [auth BE]	166	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: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	FA [auth BF]	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: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	GA [auth BG]	178	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P02359 (Escherichia coli (strain K12)) Explore P02359 Go to UniProtKB: P02359
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02359
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	HA [auth BH]	129	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7W7 (Escherichia coli (strain K12)) Explore P0A7W7 Go to UniProtKB: P0A7W7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7W7
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	IA [auth BI]	129	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: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	JA [auth BJ]	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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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R5
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	KA [auth BK]	128	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7R9 (Escherichia coli (strain K12)) Explore P0A7R9 Go to UniProtKB: P0A7R9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7R9
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	LA [auth BL]	123	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: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	MA [auth BM]	117	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7S9 (Escherichia coli (strain K12)) Explore P0A7S9 Go to UniProtKB: P0A7S9
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UniProt Group	P0A7S9
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14	NA [auth BN]	100	Escherichia coli	Mutation(s): 0

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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	OA [auth BO]	88	Escherichia coli	Mutation(s): 0

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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	PA [auth BP]	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: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	QA [auth BQ]	83	Escherichia coli	Mutation(s): 0

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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	RA [auth BR]	74	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12)) Explore P0A7T7 Go to UniProtKB: P0A7T7
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UniProt Group	P0A7T7
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	SA [auth BS]	91	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: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	TA [auth BT]	86	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12)) Explore P0A7U7 Go to UniProtKB: P0A7U7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A7U7
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Molecule	Chains	Length	Organism
Entity ID: 1
23S ribosomal RNA	A [auth A0]	2,904	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 2
5S ribosomal RNA	B [auth A9]	120	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 28
16S RIBOSOMAL RNA	BA	1,542	Escherichia coli
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Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 12.3 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

This entry supersedes: 1P85, 1P6G

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: 2015-03-18
Changes: Other
Version 1.3: 2018-01-24
Changes: Data collection, Database references, Structure summary
Version 1.4: 2019-12-18
Changes: Other
Version 1.5: 2024-02-28
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

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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.

4V47 | pdb_00004v47

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome

Literature

Study of the structural dynamics of the E. coli 70S ribosome using real space refinement

Biological Assembly 1

Macromolecules

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

Entity ID: 12

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Entity ID: 13

Entity ID: 14

Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

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Entity ID: 19

Entity ID: 20

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Entity ID: 21

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Entity ID: 22

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Entity ID: 23

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Entity ID: 24

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