4V9M | pdb_00004v9m

70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state.

PDB DOI: https://doi.org/10.2210/pdb4V9M/pdb
Entry: 4V9M supersedes: 4KDG, 4KDH, 4KDJ, 4KDK
NAKB: 4V9M

Classification: RIBOSOME
Organism(s): Thermus thermophilus HB27, Escherichia coli
Mutation(s): No

Deposited: 2013-04-25 Released: 2014-07-09
Deposition Author(s): Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free:
0.329 (Depositor), 0.325 (DCC)
R-Value Work:
0.281 (Depositor), 0.286 (DCC)
R-Value Observed:
0.281 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

(2013) Science 340: 1236086-1236086

PubMed: 23812722 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1236086
Primary Citation Related Structures:
4V9J, 4V9K, 4V9L, 4V9M

PubMed Abstract:
Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic acid reveal conformational changes occurring during intermediate states of translocation, including large-scale rotation of the 30S subunit head and body. In all complexes, the tRNA acceptor ends occupy the 50S subunit E site, while their anticodon stem loops move with the head of the 30S subunit to positions between the P and E sites, forming chimeric intermediate states. Two universally conserved bases of 16S ribosomal RNA that intercalate between bases of the mRNA may act as "pawls" of a translocational ratchet. These findings provide new insights into the molecular mechanism of ribosomal translocation.

Organizational Affiliation

Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA.

Macromolecule Content

Total Structure Weight: 4,569.12 kDa
Atom Count: 308,068
Modeled Residue Count: 23,266
Deposited Residue Count: 23,306
Unique protein chains: 54
Unique nucleic acid chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	A [auth AB], IB [auth CB]	235	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62662 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62662 Go to UniProtKB: P62662
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UniProt Group	P62662
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	B [auth AC], JB [auth CC]	207	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62663 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62663 Go to UniProtKB: P62663
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UniProt Group	P62663
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	C [auth AD], KB [auth CD]	208	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62664 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62664 Go to UniProtKB: P62664
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UniProt Group	P62664
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	D [auth AE], LB [auth CE]	151	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62665 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62665 Go to UniProtKB: P62665
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UniProt Group	P62665
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6	E [auth AF], MB [auth CF]	101	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62666 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62666 Go to UniProtKB: P62666
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UniProt Group	P62666
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	F [auth AG], NB [auth CG]	155	Thermus thermophilus HB27	Mutation(s): 0
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UniProt Group	P62667
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	G [auth AH], OB [auth CH]	138	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62668 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62668 Go to UniProtKB: P62668
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UniProt Group	P62668
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	H [auth AI], PB [auth CI]	127	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62669 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62669 Go to UniProtKB: P62669
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62669
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	I [auth AJ], QB [auth CJ]	99	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62653 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62653 Go to UniProtKB: P62653
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UniProt Group	P62653
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	J [auth AK], RB [auth CK]	119	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62654 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62654 Go to UniProtKB: P62654
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62654
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	K [auth AL], SB [auth CL]	125	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P61941 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P61941 Go to UniProtKB: P61941
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UniProt Group	P61941
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	L [auth AM], TB [auth CM]	125	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62655 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62655 Go to UniProtKB: P62655
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UniProt Group	P62655
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	M [auth AN], UB [auth CN]	60	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62656 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62656 Go to UniProtKB: P62656
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UniProt Group	P62656
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	N [auth AO], VB [auth CO]	88	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62657 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62657 Go to UniProtKB: P62657
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UniProt Group	P62657
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S16	O [auth AP], WB [auth CP]	84	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62238 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62238 Go to UniProtKB: P62238
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UniProt Group	P62238
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	P [auth AQ], XB [auth CQ]	100	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62658 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62658 Go to UniProtKB: P62658
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UniProt Group	P62658
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S18	Q [auth AR], YB [auth CR]	70	Thermus thermophilus HB27	Mutation(s): 0
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Find proteins for P62659 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62659 Go to UniProtKB: P62659
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UniProt Group	P62659
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	R [auth AS], ZB [auth CS]	79	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62660 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62660 Go to UniProtKB: P62660
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UniProt Group	P62660
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S20	AC [auth CT], S [auth AT]	99	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62661 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62661 Go to UniProtKB: P62661
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UniProt Group	P62661
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor G	EC [auth CY], W [auth AY]	687	Thermus thermophilus HB27	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: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L1	FC [auth DC], X [auth BC]	228	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72GV9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GV9 Go to UniProtKB: Q72GV9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72GV9
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	GC [auth DD], Y [auth BD]	275	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I07 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I07 Go to UniProtKB: Q72I07
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UniProt Group	Q72I07
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	HC [auth DE], Z [auth BE]	205	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I04 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I04 Go to UniProtKB: Q72I04
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UniProt Group	Q72I04
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	AA [auth BF], IC [auth DF]	208	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I05 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I05 Go to UniProtKB: Q72I05
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UniProt Group	Q72I05
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	BA [auth BG], JC [auth DG]	181	Thermus thermophilus HB27	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: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	CA [auth BH], KC [auth DH]	167	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I19 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I19 Go to UniProtKB: Q72I19
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UniProt Group	Q72I19
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10	DA [auth BJ], LC [auth DJ]	170	Thermus thermophilus HB27	Mutation(s): 0

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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L11	EA [auth BK], MC [auth DK]	140	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62442 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62442 Go to UniProtKB: P62442
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UniProt Group	P62442
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	FA [auth BN], NC [auth DN]	138	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72IN1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IN1 Go to UniProtKB: Q72IN1
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UniProt Group	Q72IN1
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	GA [auth BO], OC [auth DO]	122	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I14 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I14 Go to UniProtKB: Q72I14
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UniProt Group	Q72I14
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	HA [auth BP], PC [auth DP]	146	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I23 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I23 Go to UniProtKB: Q72I23
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UniProt Group	Q72I23
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L16	IA [auth BQ], QC [auth DQ]	141	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I11 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I11 Go to UniProtKB: Q72I11
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UniProt Group	Q72I11
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L17	JA [auth BR], RC [auth DR]	117	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I33 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I33 Go to UniProtKB: Q72I33
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UniProt Group	Q72I33
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	KA [auth BS], SC [auth DS]	99	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I20 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I20 Go to UniProtKB: Q72I20
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UniProt Group	Q72I20
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19	LA [auth BT], TC [auth DT]	138	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72JU9 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72JU9 Go to UniProtKB: Q72JU9
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UniProt Group	Q72JU9
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L20	MA [auth BU], UC [auth DU]	117	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72L76 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72L76 Go to UniProtKB: Q72L76
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UniProt Group	Q72L76
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21	NA [auth BV], VC [auth DV]	101	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72HR2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72HR2 Go to UniProtKB: Q72HR2
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UniProt Group	Q72HR2
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	OA [auth BW], WC [auth DW]	113	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I09 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I09 Go to UniProtKB: Q72I09
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UniProt Group	Q72I09
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	PA [auth BX], XC [auth DX]	93	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I06 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I06 Go to UniProtKB: Q72I06
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UniProt Group	Q72I06
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	QA [auth BY], YC [auth DY]	107	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I15 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I15 Go to UniProtKB: Q72I15
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UniProt Group	Q72I15
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L25	RA [auth BZ], ZC [auth DZ]	185	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72IA7 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IA7 Go to UniProtKB: Q72IA7
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UniProt Group	Q72IA7
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L27	AD [auth D0], SA [auth B0]	84	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72HR3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72HR3 Go to UniProtKB: Q72HR3
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UniProt Group	Q72HR3
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	BD [auth D2], TA [auth B2]	71	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I12 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I12 Go to UniProtKB: Q72I12
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UniProt Group	Q72I12
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	CD [auth D3], UA [auth B3]	60	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I22 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I22 Go to UniProtKB: Q72I22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72I22
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Reference Sequence

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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32	DD [auth D5], VA [auth B5]	59	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P62652 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore P62652 Go to UniProtKB: P62652
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62652
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Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L33	ED [auth D6], WA [auth B6]	50	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72GW3 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GW3 Go to UniProtKB: Q72GW3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72GW3
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Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34	FD [auth D7], XA [auth B7]	49	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for P80340 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore P80340 Go to UniProtKB: P80340
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P80340
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Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L35	GD [auth D8], YA [auth B8]	64	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72L77 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72L77 Go to UniProtKB: Q72L77
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72L77
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Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L36	HD [auth D9], ZA [auth B9]	37	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72I28 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72I28 Go to UniProtKB: Q72I28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72I28
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Reference Sequence

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Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7/L12	AB [auth Be], ID [auth De]	102	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72GS2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72GS2 Go to UniProtKB: Q72GS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72GS2
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Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7/L12	BB [auth Bf], CB [auth Bg], JD [auth Df], KD [auth Dg]	31	Thermus thermophilus HB27	Mutation(s): 0

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Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7/L12	DB [auth Bh], LD [auth Dh]	30	Thermus thermophilus HB27	Mutation(s): 0

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Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L28	EB [auth B1], MD [auth D1]	93	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72G84 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72G84 Go to UniProtKB: Q72G84
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72G84
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Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31	FB [auth B4], ND [auth D4]	35	Thermus thermophilus HB27	Mutation(s): 0
UniProt
Find proteins for Q72JR0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72JR0 Go to UniProtKB: Q72JR0
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UniProt Group	Q72JR0
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Molecule	Chains	Length	Organism
Entity ID: 20
ribosomal RNA 16S	BC [auth CA], T [auth AA]	1,511	Thermus thermophilus HB27
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Molecule	Chains	Length	Organism
Entity ID: 21
transfer RNA	CC [auth CW], U [auth AW]	77	Escherichia coli
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Molecule	Chains	Length	Organism
Entity ID: 22
messenger RNA	DC [auth CV], V [auth AV]	23	Thermus thermophilus HB27
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Molecule	Chains	Length	Organism
Entity ID: 58
23S ribosomal RNA	GB [auth BA], OD [auth DA]	2,879	Thermus thermophilus HB27
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Molecule	Chains	Length	Organism
Entity ID: 59
5S ribosomal RNA	HB [auth BB], PD [auth DB]	119	Thermus thermophilus HB27
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUA Query on FUA Download:Ideal Coordinates CCD File SDF format, chain QD [auth AY] SDF format, chain SD [auth CY] MOL2 format, chain QD [auth AY] MOL2 format, chain SD [auth CY] mmCIF format, chain QD [auth AY] mmCIF format, chain SD [auth CY]	QD [auth AY], SD [auth CY]	FUSIDIC ACID C₃₁ H₄₈ O₆ IECPWNUMDGFDKC-MZJAQBGESA-N		Interactions Focus chain QD [auth AY] Focus chain SD [auth CY] Interactions & Density Focus chain QD [auth AY] Focus chain SD [auth CY]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain RD [auth AY] SDF format, chain TD [auth CY] MOL2 format, chain RD [auth AY] MOL2 format, chain TD [auth CY] mmCIF format, chain RD [auth AY] mmCIF format, chain TD [auth CY]	RD [auth AY], TD [auth CY]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain RD [auth AY] Focus chain TD [auth CY] Interactions & Density Focus chain RD [auth AY] Focus chain TD [auth CY]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.00 Å
R-Value Free: 0.329 (Depositor), 0.325 (DCC)
R-Value Work: 0.281 (Depositor), 0.286 (DCC)
R-Value Observed: 0.281 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 307.2101	α = 90
b = 670.4372	β = 92.374
c = 350.4025	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
CNS	refinement
XDS	data reduction
SCALA	data scaling

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: 4KDG, 4KDH, 4KDJ, 4KDK

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: 2017-06-28
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-11-06
Changes: Structure summary

RCSB PDB is hosted by

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Nucleic Acid Knowledgebase

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

4V9M | pdb_00004v9m

70S Ribosome translocation intermediate FA-4.2A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state.

Literature

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Biological Assembly 1

Biological Assembly 2

Macromolecules

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UniProt

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