4V9J

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 

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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

  • DOI: https://doi.org/10.1126/science.1236086
  • Primary Citation of 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2A [auth AB],
JB [auth CB]
235Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC],
KB [auth CC]
207Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth AD],
LB [auth CD]
208Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth AE],
MB [auth CE]
151Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth AF],
NB [auth CF]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG],
OB [auth CG]
155Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth AH],
PB [auth CH]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI],
QB [auth CI]
127Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth AJ],
RB [auth CJ]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth AK],
SB [auth CK]
119Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth AL],
TB [auth CL]
125Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM],
UB [auth CM]
125Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth AN],
VB [auth CN]
60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth AO],
WB [auth CO]
88Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth AP],
XB [auth CP]
84Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth AQ],
YB [auth CQ]
100Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth AR],
ZB [auth CR]
70Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AC [auth CS],
R [auth AS]
79Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BC [auth CT],
S [auth AT]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GFC [auth CY],
W [auth AY]
687Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ViomycinGC [auth CU],
X [auth AU]
6StreptomycesMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1HC [auth DC],
Y [auth BC]
228Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2IC [auth DD],
Z [auth BD]
275Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AA [auth BE],
JC [auth DE]
205Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4BA [auth BF],
KC [auth DF]
208Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth BG],
LC [auth DG]
181Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6DA [auth BH],
MC [auth DH]
167Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EA [auth BJ],
NC [auth DJ]
170Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11FA [auth BK],
OC [auth DK]
140Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14GA [auth BO],
PC [auth DO]
122Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15HA [auth BP],
QC [auth DP]
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16IA [auth BQ],
RC [auth DQ]
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17JA [auth BR],
SC [auth DR]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18KA [auth BS],
TC [auth DS]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19LA [auth BT],
UC [auth DT]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20MA [auth BU],
VC [auth DU]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21NA [auth BV],
WC [auth DV]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22OA [auth BW],
XC [auth DW]
113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PA [auth BX],
YC [auth DX]
93Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24QA [auth BY],
ZC [auth DY]
107Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AD [auth DZ],
RA [auth BZ]
185Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BD [auth D0],
SA [auth B0]
84Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CD [auth D1],
TA [auth B1]
93Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31DD [auth D4],
UA [auth B4]
35Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13ED [auth DN],
VA [auth BN]
138Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29FD [auth D2],
WA [auth B2]
71Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30GD [auth D3],
XA [auth B3]
60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32HD [auth D5],
YA [auth B5]
59Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ID [auth D6],
ZA [auth B6]
50Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth B7],
JD [auth D7]
49Thermus thermophilus HB27Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth B8],
KD [auth D8]
64Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth B9],
LD [auth D9]
37Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12DB [auth Be],
MD [auth De]
103Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12EB [auth Bf],
FB [auth Bg],
ND [auth Df],
OD [auth Dg]
31Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12GB [auth Bh],
PD [auth Dh]
30Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 20
MoleculeChains LengthOrganismImage
16S ribosomal RNACC [auth CA],
T [auth AA]
1,511Thermus thermophilus HB27
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Entity ID: 21
MoleculeChains LengthOrganismImage
messenger RNADC [auth CV],
U [auth AV]
18Thermus thermophilus HB27
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNA-MetEC [auth CW],
V [auth AW]
77Escherichia coli
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Entity ID: 59
MoleculeChains LengthOrganismImage
5S ribosomal RNAHB [auth BB],
QD [auth DB]
119Thermus thermophilus HB27
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Entity ID: 60
MoleculeChains LengthOrganismImage
23S ribosomal RNAIB [auth BA],
RD [auth DA]
2,879Thermus thermophilus HB27
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Small Molecules
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
5OH
Query on 5OH
GC [auth CU],
X [auth AU]
L-PEPTIDE LINKINGC6 H12 N4 O3ALA
DPP
Query on DPP
GC [auth CU],
X [auth AU]
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
GC [auth CU],
X [auth AU]
L-PEPTIDE LINKINGC6 H14 N2 O2LYS
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.264 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 302.3911α = 90
b = 683.9183β = 89.9983
c = 356.6977γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2017-06-28
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection