4V5F | pdb_00004v5f

The structure of the ribosome with elongation factor G trapped in the post-translocational state

PDB DOI: https://doi.org/10.2210/pdb4V5F/pdb
Entry: 4V5F supersedes: 2WRI, 2WRJ, 2WRK, 2WRL
NAKB: 4V5F

Classification: RIBOSOME
Organism(s): Thermus thermophilus HB8, Escherichia coli K-12, synthetic construct
Mutation(s): No

Deposited: 2009-09-01 Released: 2014-07-09
Deposition Author(s): Gao, Y.-G., Selmer, M., Dunham, C.M., Weixlbaumer, A., Kelley, A.C., Ramakrishnan, V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free:
0.260 (Depositor), 0.223 (DCC)
R-Value Work:
0.227 (Depositor), 0.224 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The structure of the ribosome with elongation factor G trapped in the posttranslocational state.

Gao, Y.G., Selmer, M., Dunham, C.M., Weixlbaumer, A., Kelley, A.C., Ramakrishnan, V.

(2009) Science 326: 694-699

PubMed: 19833919 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1179709
Primary Citation Related Structures:
4V5F

PubMed Abstract:
Elongation factor G (EF-G) is a guanosine triphosphatase (GTPase) that plays a crucial role in the translocation of transfer RNAs (tRNAs) and messenger RNA (mRNA) during translation by the ribosome. We report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with EF-G in the posttranslocational state using the antibiotic fusidic acid. Fusidic acid traps EF-G in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. The interaction of EF-G with ribosomal elements implicated in stimulating catalysis, such as the L10-L12 stalk and the L11 region, and of domain IV of EF-G with the tRNA at the peptidyl-tRNA binding site (P site) and with mRNA shed light on the role of these elements in EF-G function. The stabilization of the mobile stalks of the ribosome also results in a more complete description of its structure.

Organizational Affiliation

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK.

Macromolecule Content

Total Structure Weight: 4,772.3 kDa
Atom Count: 311,552
Modeled Residue Count: 23,526
Deposited Residue Count: 24,788
Unique protein chains: 53
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S2	B [auth AB], LB [auth CB]	256	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80371 Go to UniProtKB: P80371
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UniProt Group	P80371
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S3	C [auth AC], MB [auth CC]	239	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P80372 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80372 Go to UniProtKB: P80372
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UniProt Group	P80372
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S4	D [auth AD], NB [auth CD]	209	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80373 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80373 Go to UniProtKB: P80373
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UniProt Group	P80373
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S5	E [auth AE], OB [auth CE]	162	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ5 Go to UniProtKB: Q5SHQ5
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ5
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S6	F [auth AF], PB [auth CF]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP8 Go to UniProtKB: Q5SLP8
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UniProt Group	Q5SLP8
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S7	G [auth AG], QB [auth CG]	156	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P17291 Go to UniProtKB: P17291
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UniProt Group	P17291
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S8	H [auth AH], RB [auth CH]	138	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY9 Go to UniProtKB: P0DOY9
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UniProt Group	P0DOY9
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S9	I [auth AI], SB [auth CI]	128	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80374 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80374 Go to UniProtKB: P80374
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UniProt Group	P80374
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S10	J [auth AJ], TB [auth CJ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN7 Go to UniProtKB: Q5SHN7
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UniProt Group	Q5SHN7
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S11	K [auth AK], UB [auth CK]	129	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80376 Go to UniProtKB: P80376
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UniProt Group	P80376
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S12	L [auth AL], VB [auth CL]	132	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN3 Go to UniProtKB: Q5SHN3
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UniProt Group	Q5SHN3
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S13	M [auth AM], WB [auth CM]	126	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P80377 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80377 Go to UniProtKB: P80377
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UniProt Group	P80377
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S14 TYPE Z	N [auth AN], XB [auth CN]	61	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY6 Go to UniProtKB: P0DOY6
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UniProt Group	P0DOY6
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S15	O [auth AO], YB [auth CO]	89	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ76 Go to UniProtKB: Q5SJ76
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UniProt Group	Q5SJ76
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S16	P [auth AP], ZB [auth CP]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH3 Go to UniProtKB: Q5SJH3
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UniProt Group	Q5SJH3
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S17	AC [auth CQ], Q [auth AQ]	105	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY7 Go to UniProtKB: P0DOY7
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UniProt Group	P0DOY7
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S18	BC [auth CR], R [auth AR]	88	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLQ0 Go to UniProtKB: Q5SLQ0
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UniProt Group	Q5SLQ0
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S19	CC [auth CS], S [auth AS]	93	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2 Go to UniProtKB: Q5SHP2
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UniProt Group	Q5SHP2
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN S20	DC [auth CT], T [auth AT]	106	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80380 Go to UniProtKB: P80380
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UniProt Group	P80380
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S RIBOSOMAL PROTEIN THX	EC [auth CU], U [auth AU]	27	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SIH3 Go to UniProtKB: Q5SIH3
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UniProt Group	Q5SIH3
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR G	IC [auth CY], Y [auth AY]	691	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN5 Go to UniProtKB: Q5SHN5
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UniProt Group	Q5SHN5
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L27	JC [auth D0], Z [auth B0]	85	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60493 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60493 Go to UniProtKB: P60493
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UniProt Group	P60493
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L28	AA [auth B1], KC [auth D1]	98	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60494 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60494 Go to UniProtKB: P60494
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UniProt Group	P60494
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L29	BA [auth B2], LC [auth D2]	72	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP6 Go to UniProtKB: Q5SHP6
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UniProt Group	Q5SHP6
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L30	CA [auth B3], MC [auth D3]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ6 Go to UniProtKB: Q5SHQ6
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UniProt Group	Q5SHQ6
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L31	DA [auth B4], NC [auth D4]	71	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJE1 Go to UniProtKB: Q5SJE1
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UniProt Group	Q5SJE1
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L32	EA [auth B5], OC [auth D5]	60	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80339 Go to UniProtKB: P80339
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UniProt Group	P80339
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L33	FA [auth B6], PC [auth D6]	54	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P35871 Go to UniProtKB: P35871
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UniProt Group	P35871
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L34	GA [auth B7], QC [auth D7]	49	Thermus thermophilus HB8	Mutation(s): 0
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UniProt Group	P80340
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L35	HA [auth B8], RC [auth D8]	65	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKU1 Go to UniProtKB: Q5SKU1
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UniProt Group	Q5SKU1
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L36	IA [auth B9], SC [auth D9]	37	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHR2 Go to UniProtKB: Q5SHR2
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UniProt Group	Q5SHR2
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L1	LA [auth BC], VC [auth DC]	229	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP7 Go to UniProtKB: Q5SLP7
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UniProt Group	Q5SLP7
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L2	MA [auth BD], WC [auth DD]	276	Thermus thermophilus HB8	Mutation(s): 0
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Find proteins for P60405 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60405 Go to UniProtKB: P60405
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UniProt Group	P60405
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L3	NA [auth BE], XC [auth DE]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN8 Go to UniProtKB: Q5SHN8
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UniProt Group	Q5SHN8
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L4	OA [auth BF], YC [auth DF]	210	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHN9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHN9 Go to UniProtKB: Q5SHN9
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UniProt Group	Q5SHN9
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L5	PA [auth BG], ZC [auth DG]	182	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ0 Go to UniProtKB: Q5SHQ0
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UniProt Group	Q5SHQ0
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L6	AD [auth DH], QA [auth BH]	180	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P0DOY8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P0DOY8 Go to UniProtKB: P0DOY8
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UniProt Group	P0DOY8
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L10	BD [auth DJ], RA [auth BJ]	173	Thermus thermophilus HB8	Mutation(s): 0

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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L11	CD [auth DK], SA [auth BK]	147	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SLP6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLP6 Go to UniProtKB: Q5SLP6
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UniProt Group	Q5SLP6
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L12	DD [auth DL] ED [auth DM] IB [auth Bl] JB [auth Bm] SD [auth Dl] DD [auth DL], ED [auth DM], IB [auth Bl], JB [auth Bm], SD [auth Dl], TA [auth BL], TD [auth Dm], UA [auth BM]	125	Thermus thermophilus HB8	Mutation(s): 0

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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L13	FD [auth DN], VA [auth BN]	140	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60488 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60488 Go to UniProtKB: P60488
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UniProt Group	P60488
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L14	GD [auth DO], WA [auth BO]	122	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP8 Go to UniProtKB: Q5SHP8
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UniProt Group	Q5SHP8
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L15	HD [auth DP], XA [auth BP]	150	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ7 Go to UniProtKB: Q5SHQ7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ7
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L16	ID [auth DQ], YA [auth BQ]	141	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60489 Go to UniProtKB: P60489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60489
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Reference Sequence

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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L17	JD [auth DR], ZA [auth BR]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q9Z9H5 Go to UniProtKB: Q9Z9H5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Z9H5
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Reference Sequence

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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L18	AB [auth BS], KD [auth DS]	112	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHQ4 Go to UniProtKB: Q5SHQ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHQ4
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Reference Sequence

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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L19	BB [auth BT], LD [auth DT]	146	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60490 Go to UniProtKB: P60490
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60490
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Reference Sequence

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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L20	CB [auth BU], MD [auth DU]	118	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60491 Go to UniProtKB: P60491
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60491
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L21	DB [auth BV], ND [auth DV]	101	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P60492 Go to UniProtKB: P60492
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60492
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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L22	EB [auth BW], OD [auth DW]	113	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP3 Go to UniProtKB: Q5SHP3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHP3
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Reference Sequence

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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L23	FB [auth BX], PD [auth DX]	96	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP0 Go to UniProtKB: Q5SHP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHP0
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L24	GB [auth BY], QD [auth DY]	110	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP9 Go to UniProtKB: Q5SHP9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHP9
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Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
50S RIBOSOMAL PROTEIN L25	HB [auth BZ], RD [auth DZ]	206	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ1 Go to UniProtKB: Q5SHZ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SHZ1
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
16S ribosomal RNA	A [auth AA], KB [auth CA]	1,522	Thermus thermophilus HB8
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Molecule	Chains	Length	Organism
Entity ID: 22
E-SITE TRNA FMET OR P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)	FC [auth CV], GC [auth CW], V [auth AV], W [auth AW]	77	Escherichia coli K-12
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Molecule	Chains	Length	Organism
Entity ID: 23
MRNA	HC [auth CX], X [auth AX]	25	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 35
23S RIBOSOMAL RNA	JA [auth BA], TC [auth DA]	2,915	Thermus thermophilus HB8
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Molecule	Chains	Length	Organism
Entity ID: 36
5S RIBOSOMAL RNA	KA [auth BB], UC [auth DB]	122	Thermus thermophilus HB8
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUA Query on FUA Download:Ideal Coordinates CCD File SDF format, chain XD [auth AY] SDF format, chain EE [auth CY] MOL2 format, chain XD [auth AY] MOL2 format, chain EE [auth CY] mmCIF format, chain XD [auth AY] mmCIF format, chain EE [auth CY]	EE [auth CY], XD [auth AY]	FUSIDIC ACID C₃₁ H₄₈ O₆ IECPWNUMDGFDKC-MZJAQBGESA-N		Interactions Focus chain EE [auth CY] Focus chain XD [auth AY] Interactions & Density Focus chain EE [auth CY] Focus chain XD [auth AY]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain YD [auth AY] SDF format, chain FE [auth CY] MOL2 format, chain YD [auth AY] MOL2 format, chain FE [auth CY] mmCIF format, chain YD [auth AY] mmCIF format, chain FE [auth CY]	FE [auth CY], YD [auth AY]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain FE [auth CY] Focus chain YD [auth AY] Interactions & Density Focus chain FE [auth CY] Focus chain YD [auth AY]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain ZD [auth B4] SDF format, chain VD [auth AN] SDF format, chain UD [auth AD] SDF format, chain HE [auth D9] SDF format, chain GE [auth D4] SDF format, chain CE [auth CN] SDF format, chain BE [auth CD] SDF format, chain AE [auth B9] MOL2 format, chain ZD [auth B4] MOL2 format, chain VD [auth AN] MOL2 format, chain UD [auth AD] MOL2 format, chain HE [auth D9] MOL2 format, chain GE [auth D4] MOL2 format, chain CE [auth CN] MOL2 format, chain BE [auth CD] MOL2 format, chain AE [auth B9] mmCIF format, chain ZD [auth B4] mmCIF format, chain VD [auth AN] mmCIF format, chain UD [auth AD] mmCIF format, chain HE [auth D9] mmCIF format, chain GE [auth D4] mmCIF format, chain CE [auth CN] mmCIF format, chain BE [auth CD] mmCIF format, chain AE [auth B9]	AE [auth B9] BE [auth CD] CE [auth CN] GE [auth D4] HE [auth D9] AE [auth B9], BE [auth CD], CE [auth CN], GE [auth D4], HE [auth D9], UD [auth AD], VD [auth AN], ZD [auth B4]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AE [auth B9] Focus chain BE [auth CD] Focus chain CE [auth CN] Focus chain GE [auth D4] Focus chain HE [auth D9] Focus chain UD [auth AD] Focus chain VD [auth AN] Focus chain ZD [auth B4] Interactions & Density Focus chain AE [auth B9] Focus chain BE [auth CD] Focus chain CE [auth CN] Focus chain GE [auth D4] Focus chain HE [auth D9] Focus chain UD [auth AD] Focus chain VD [auth AN] Focus chain ZD [auth B4]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain WD [auth AY] SDF format, chain DE [auth CY] MOL2 format, chain WD [auth AY] MOL2 format, chain DE [auth CY] mmCIF format, chain WD [auth AY] mmCIF format, chain DE [auth CY]	DE [auth CY], WD [auth AY]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DE [auth CY] Focus chain WD [auth AY] Interactions & Density Focus chain DE [auth CY] Focus chain WD [auth AY]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.260 (Depositor), 0.223 (DCC)
R-Value Work: 0.227 (Depositor), 0.224 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 291.839	α = 90
b = 270.358	β = 91.73
c = 402.363	γ = 90

Software Package:

Software Name	Purpose
PHASER	model building
CNS	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

This entry supersedes: 2WRI, 2WRJ, 2WRK, 2WRL

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: 2015-10-07
Changes: Refinement description
Version 1.3: 2018-03-14
Changes: Database references, Source and taxonomy, Structure summary
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-16
Changes: Structure summary

RCSB PDB is hosted by

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RCSB Partners
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.

4V5F | pdb_00004v5f

The structure of the ribosome with elongation factor G trapped in the post-translocational state

Literature

The structure of the ribosome with elongation factor G trapped in the posttranslocational state.

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 2

UniProt

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Entity ID: 3

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

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Entity ID: 15

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Entity ID: 16

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Entity ID: 17

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Entity ID: 18

UniProt

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Entity ID: 19

UniProt

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Entity ID: 20