4W29 | pdb_00004w29

70S ribosome translocation intermediate containing elongation factor EFG/GDP/fusidic acid, mRNA, and tRNAs trapped in the AP/AP pe/E chimeric hybrid state.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.331 (Depositor), 0.330 (DCC) 
  • R-Value Work: 
    0.295 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 
    0.296 (Depositor) 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

How the ribosome hands the A-site tRNA to the P site during EF-G-catalyzed translocation.

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

(2014) Science 345: 1188-1191

  • DOI: https://doi.org/10.1126/science.1255030
  • Primary Citation of Related Structures:  
    4W29

  • PubMed Abstract: 

    Coupled translocation of messenger RNA and transfer RNA (tRNA) through the ribosome, a process catalyzed by elongation factor EF-G, is a crucial step in protein synthesis. The crystal structure of a bacterial translocation complex describes the binding states of two tRNAs trapped in mid-translocation. The deacylated P-site tRNA has moved into a partly translocated pe/E chimeric hybrid state. The anticodon stem-loop of the A-site tRNA is captured in transition toward the 30S P site, while its 3' acceptor end contacts both the A and P loops of the 50S subunit, forming an ap/ap chimeric hybrid state. The structure shows how features of ribosomal RNA rearrange to hand off the A-site tRNA to the P site, revealing an active role for ribosomal RNA in the translocation process.


  • Organizational Affiliation
    • Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, 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 
UniProt
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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 
UniProt
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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 HB8Mutation(s): 0 
UniProt
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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 HB8Mutation(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 HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GCC [auth CY],
T [auth AY]
687Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1HC [auth DC],
Y [auth BC]
228Thermus thermophilusMutation(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 HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5CA [auth BG],
LC [auth DG]
181Thermus thermophilusMutation(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 L13GA [auth BN],
PC [auth DN]
139Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth BO],
QC [auth DO]
122Thermus thermophilusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth BP],
RC [auth DP]
146Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth BQ],
SC [auth DQ]
141Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth BR],
TC [auth DR]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth BS],
UC [auth DS]
99Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth BT],
VC [auth DT]
138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth BU],
WC [auth DU]
117Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth BV],
XC [auth DV]
101Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth BW],
YC [auth DW]
113Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth BX],
ZC [auth DX]
93Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AD [auth DY],
RA [auth BY]
107Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25BD [auth DZ],
SA [auth BZ]
185Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CD [auth D0],
TA [auth B0]
84Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28DD [auth D1],
UA [auth B1]
93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29ED [auth D2],
VA [auth B2]
71Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30FD [auth D3],
WA [auth B3]
60Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31GD [auth D4],
XA [auth B4]
35Thermus 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 HB8Mutation(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 HB8Mutation(s): 0 
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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: 21
MoleculeChains LengthOrganismImage
16S Ribosomal RNADC [auth CA],
U [auth AA]
1,511Thermus thermophilus HB27
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Entity ID: 22
MoleculeChains LengthOrganismImage
tRNAFC [auth CW],
V [auth AW]
77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNAEC [auth CV],
W [auth AV]
36Escherichia coli str. K-12 substr. MG1655
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Entity ID: 24
MoleculeChains LengthOrganismImage
tRNAGC [auth CX],
X [auth AX]
78Escherichia coli
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Entity ID: 59
MoleculeChains LengthOrganismImage
23S Ribosomal RNAHB [auth BA],
QD [auth DA]
2,879Thermus thermophilus HB27
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Entity ID: 60
MoleculeChains LengthOrganismImage
5S Ribosomal RNAIB [auth BB],
RD [auth DB]
119Thermus thermophilus HB27
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMY
Query on NMY

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CE [auth CA]
DE [auth DA]
UD [auth AA]
WD [auth BA]
XD [auth BA]
CE [auth CA],
DE [auth DA],
UD [auth AA],
WD [auth BA],
XD [auth BA],
YD [auth BA]
NEOMYCIN
C23 H46 N6 O13
PGBHMTALBVVCIT-VCIWKGPPSA-N
FUA
Query on FUA

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AE [auth CY],
TD [auth AY]
FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
GDP
Query on GDP

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SD [auth AY],
ZD [auth CY]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

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BE [auth CY],
VD [auth BA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.331 (Depositor), 0.330 (DCC) 
  • R-Value Work:  0.295 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 0.296 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 306.919α = 90
b = 677.002β = 89.9
c = 356.78γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata 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: 2014-10-01
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2017-05-31
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description