4V5F

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 
    0.260 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Models: experimental
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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

  • DOI: https://doi.org/10.1126/science.1179709
  • Primary Citation of 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.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB],
LB [auth CB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC],
MB [auth CC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD],
NB [auth CD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE],
OB [auth CE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF],
PB [auth CF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG],
QB [auth CG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH],
RB [auth CH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AI],
SB [auth CI]		128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AJ],
TB [auth CJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AK],
UB [auth CK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AL],
VB [auth CL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM],
WB [auth CM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZN [auth AN],
XB [auth CN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AO],
YB [auth CO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AP],
ZB [auth CP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17AC [auth CQ],
Q [auth AQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18BC [auth CR],
R [auth AR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19CC [auth CS],
S [auth AS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20DC [auth CT],
T [auth AT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXEC [auth CU],
U [auth AU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR GIC [auth CY],
Y [auth AY]		691Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27JC [auth D0],
Z [auth B0]		85Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28AA [auth B1],
KC [auth D1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29BA [auth B2],
LC [auth D2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30CA [auth B3],
MC [auth D3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31DA [auth B4],
NC [auth D4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32EA [auth B5],
OC [auth D5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33FA [auth B6],
PC [auth D6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34GA [auth B7],
QC [auth D7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35HA [auth B8],
RC [auth D8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36IA [auth B9],
SC [auth D9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1LA [auth BC],
VC [auth DC]		229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2MA [auth BD],
WC [auth DD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3NA [auth BE],
XC [auth DE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4OA [auth BF],
YC [auth DF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5PA [auth BG],
ZC [auth DG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6AD [auth DH],
QA [auth BH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10BD [auth DJ],
RA [auth BJ]		173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11CD [auth DK],
SA [auth BK]		147Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L12125Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13FD [auth DN],
VA [auth BN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14GD [auth DO],
WA [auth BO]		122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15HD [auth DP],
XA [auth BP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16ID [auth DQ],
YA [auth BQ]		141Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17JD [auth DR],
ZA [auth BR]		118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18AB [auth BS],
KD [auth DS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19BB [auth BT],
LD [auth DT]		146Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20CB [auth BU],
MD [auth DU]		118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21DB [auth BV],
ND [auth DV]		101Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22EB [auth BW],
OD [auth DW]		113Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23FB [auth BX],
PD [auth DX]		96Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24GB [auth BY],
QD [auth DY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25HB [auth BZ],
RD [auth DZ]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FUA
Query on FUA
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EE [auth CY],
XD [auth AY]		FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
GDP
Query on GDP
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FE [auth CY],
YD [auth AY]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AE [auth B9]
BE [auth CD]
CE [auth CN]
GE [auth D4]
HE [auth D9]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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DE [auth CY],
WD [auth AY]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free:  0.260 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 291.839α = 90
b = 270.358β = 91.73
c = 402.363γ = 90
Software Package:
Software NamePurpose
PHASERmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FUAClick on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

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