4V9M

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2A [auth AB], IB [auth CB]235Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsBrps2TT_C0509
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth AC], JB [auth CC]207Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsCrps3TT_C1322
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth AD], KB [auth CD]208Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsDrps4TT_C1301
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth AE], LB [auth CE]151Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsErps5TT_C1311
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth AF], MB [auth CF]101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsFrps6TT_C1740
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth AG], NB [auth CG]155Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsGrps7TT_C1332
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth AH], OB [auth CH]138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsHrps8TT_C1314
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth AI], PB [auth CI]127Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsIrps9TT_C1100
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth AJ], QB [auth CJ]99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsJrps10TT_C1329
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth AK], RB [auth CK]119Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsKrps11TT_C1302
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth AL], SB [auth CL]125Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsLrps12TT_C1333
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth AM], TB [auth CM]125Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsMrps13TT_C1303
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZM [auth AN], UB [auth CN]60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsZrps14rpsNTT_C1315
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth AO], VB [auth CO]88Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsOrps15TT_C0773
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth AP], WB [auth CP]84Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsPrps16TT_C0673
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth AQ], XB [auth CQ]100Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsQrps17TT_C1319
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth AR], YB [auth CR]70Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsRrps18TT_C1742
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth AS], ZB [auth CS]79Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsSrps19TT_C1324
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth AT], AC [auth CT]99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpsTrps20TT_C1031
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor GW [auth AY], EC [auth CY]687Thermus thermophilus HB27Mutation(s): 0 
Gene Names: fusATT_C1331
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1X [auth BC], FC [auth DC]228Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplATT_C1739
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2Y [auth BD], GC [auth DD]275Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplBTT_C1325
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3Z [auth BE], HC [auth DE]205Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplCTT_C1328
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4AA [auth BF], IC [auth DF]208Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplDTT_C1327
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth BG], JC [auth DG]181Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplETT_C1316
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6CA [auth BH], KC [auth DH]167Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplFTT_C1313
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10DA [auth BJ], LC [auth DJ]170Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11EA [auth BK], MC [auth DK]140Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplKTT_C1738
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13FA [auth BN], NC [auth DN]138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplMTT_C1101
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14GA [auth BO], OC [auth DO]122Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplNTT_C1318
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15HA [auth BP], PC [auth DP]146Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplOTT_C1309
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16IA [auth BQ], QC [auth DQ]141Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplPTT_C1321
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17JA [auth BR], RC [auth DR]117Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplQTT_C1299
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18KA [auth BS], SC [auth DS]99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplRTT_C1312
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19LA [auth BT], TC [auth DT]138Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplSTT_C0669
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20MA [auth BU], UC [auth DU]117Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplTTT_C0185
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Entity ID: 40
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50S ribosomal protein L21NA [auth BV], VC [auth DV]101Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplUTT_C1424
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Entity ID: 41
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50S ribosomal protein L22OA [auth BW], WC [auth DW]113Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplVTT_C1323
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23PA [auth BX], XC [auth DX]93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplWTT_C1326
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24QA [auth BY], YC [auth DY]107Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplXTT_C1317
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Entity ID: 44
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50S ribosomal protein L25RA [auth BZ], ZC [auth DZ]185Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplYctcTT_C1225
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Entity ID: 45
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50S ribosomal protein L27SA [auth B0], AD [auth D0]84Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmATT_C1423
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Entity ID: 46
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50S ribosomal protein L29TA [auth B2], BD [auth D2]71Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmCTT_C1320
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Entity ID: 47
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50S ribosomal protein L30UA [auth B3], CD [auth D3]60Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmDTT_C1310
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth B5], DD [auth D5]59Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmFrpl32TT_C0050
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Entity ID: 49
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50S ribosomal protein L33WA [auth B6], ED [auth D6]50Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmGTT_C1735
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Entity ID: 50
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50S ribosomal protein L34XA [auth B7], FD [auth D7]49Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 51
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50S ribosomal protein L35YA [auth B8], GD [auth D8]64Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmITT_C0184
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Entity ID: 52
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50S ribosomal protein L36ZA [auth B9], HD [auth D9]37Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmJTT_C1304
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12AB [auth Be], ID [auth De]102Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rplLTT_C1776
UniProt
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12BB [auth Bf], CB [auth Bg], JD [auth Df], KD [auth Dg]31Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12DB [auth Bh], LD [auth Dh]30Thermus thermophilus HB27Mutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28EB [auth B1], MD [auth D1]93Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmBTT_C1964
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Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31FB [auth B4], ND [auth D4]35Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpmETT_C0708
UniProt
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
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Entity ID: 20
MoleculeChainsLengthOrganismImage
ribosomal RNA 16ST [auth AA], BC [auth CA]1511Thermus thermophilus HB27
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Entity ID: 21
MoleculeChainsLengthOrganismImage
transfer RNAU [auth AW], CC [auth CW]77Escherichia coli
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Entity ID: 22
MoleculeChainsLengthOrganismImage
messenger RNAV [auth AV], DC [auth CV]23Thermus thermophilus HB27
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Entity ID: 58
MoleculeChainsLengthOrganismImage
23S ribosomal RNAGB [auth BA], OD [auth DA]2879Thermus thermophilus HB27
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Entity ID: 59
MoleculeChainsLengthOrganismImage
5S ribosomal RNAHB [auth BB], PD [auth DB]119Thermus thermophilus HB27
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUA
Query on FUA

Download Ideal Coordinates CCD File 
QD [auth AY], SD [auth CY]FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
GDP
Query on GDP

Download Ideal Coordinates CCD File 
RD [auth AY], TD [auth CY]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 307.2101α = 90
b = 670.4372β = 92.374
c = 350.4025γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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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