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 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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.



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Entity ID: 2
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30S RIBOSOMAL PROTEIN S2B [auth AB], LB [auth CB]256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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30S RIBOSOMAL PROTEIN S3C [auth AC], MB [auth CC]239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
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30S RIBOSOMAL PROTEIN S4D [auth AD], NB [auth CD]209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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30S RIBOSOMAL PROTEIN S5E [auth AE], OB [auth CE]162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
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30S RIBOSOMAL PROTEIN S6F [auth AF], PB [auth CF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S7G [auth AG], QB [auth CG]156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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30S RIBOSOMAL PROTEIN S8H [auth AH], RB [auth CH]138Thermus thermophilus HB8Mutation(s): 0 
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30S RIBOSOMAL PROTEIN S9I [auth AI], SB [auth CI]128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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30S RIBOSOMAL PROTEIN S10J [auth AJ], TB [auth CJ]105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11K [auth AK], UB [auth CK]129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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30S RIBOSOMAL PROTEIN S12L [auth AL], VB [auth CL]132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13M [auth AM], WB [auth CM]126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S14 TYPE ZN [auth AN], XB [auth CN]61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S15O [auth AO], YB [auth CO]89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S16P [auth AP], ZB [auth CP]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S17Q [auth AQ], AC [auth CQ]105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S18R [auth AR], BC [auth CR]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S19S [auth AS], CC [auth CS]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S20T [auth AT], DC [auth CT]106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
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30S RIBOSOMAL PROTEIN THXU [auth AU], EC [auth CU]27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 24
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ELONGATION FACTOR GY [auth AY], IC [auth CY]691Thermus thermophilus HB8Mutation(s): 0 
Gene Names: fusAfusTTHA1695
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Entity ID: 25
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50S RIBOSOMAL PROTEIN L27Z [auth B0], JC [auth D0]85Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 26
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50S RIBOSOMAL PROTEIN L28AA [auth B1], KC [auth D1]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L29BA [auth B2], LC [auth D2]72Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30CA [auth B3], MC [auth D3]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L31DA [auth B4], NC [auth D4]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L32EA [auth B5], OC [auth D5]60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L33FA [auth B6], PC [auth D6]54Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L34GA [auth B7], QC [auth D7]49Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L35HA [auth B8], RC [auth D8]65Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 34
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50S RIBOSOMAL PROTEIN L36IA [auth B9], SC [auth D9]37Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 37
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50S RIBOSOMAL PROTEIN L1LA [auth BC], VC [auth DC]229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L2MA [auth BD], WC [auth DD]276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L3NA [auth BE], XC [auth DE]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 40
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50S RIBOSOMAL PROTEIN L4OA [auth BF], YC [auth DF]210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L5PA [auth BG], ZC [auth DG]182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L6QA [auth BH], AD [auth DH]180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L10RA [auth BJ], BD [auth DJ]173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L11SA [auth BK], CD [auth DK]147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKTTHA0247
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50S RIBOSOMAL PROTEIN L12TA [auth BL], UA [auth BM], IB [auth Bl], JB [auth Bm], DD [auth DL], ED [auth DM], SD [auth Dl], TD [auth Dm]125Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L13VA [auth BN], FD [auth DN]140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L14WA [auth BO], GD [auth DO]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L15XA [auth BP], HD [auth DP]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 49
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50S RIBOSOMAL PROTEIN L16YA [auth BQ], ID [auth DQ]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 50
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50S RIBOSOMAL PROTEIN L17ZA [auth BR], JD [auth DR]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 51
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50S RIBOSOMAL PROTEIN L18AB [auth BS], KD [auth DS]112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 52
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50S RIBOSOMAL PROTEIN L19BB [auth BT], LD [auth DT]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L20CB [auth BU], MD [auth DU]118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21DB [auth BV], ND [auth DV]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22EB [auth BW], OD [auth DW]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23FB [auth BX], PD [auth DX]96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24GB [auth BY], QD [auth DY]110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25HB [auth BZ], RD [auth DZ]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth AA], KB [auth CA]1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
E-SITE TRNA FMET OR P-SITE TRNA FMET (UNMODIFIED BASES EXCEPT FOR THYMINE 54)V [auth AV], W [auth AW], FC [auth CV], GC [auth CW]77Escherichia coli K-12
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Entity ID: 23
MoleculeChainsLengthOrganismImage
MRNAX [auth AX], HC [auth CX]25synthetic construct
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Entity ID: 35
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNAJA [auth BA], TC [auth DA]2915Thermus thermophilus HB8
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Entity ID: 36
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNAKA [auth BB], UC [auth DB]122Thermus thermophilus HB8
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Small Molecules
Ligands 4 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
ZN
Query on ZN

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AE [auth B9], BE [auth CD], CE [auth CN], GE [auth D4], HE [auth D9], UD [auth AD], VD [auth AN], ZD [auth B4]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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DE [auth CY], WD [auth AY]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • 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

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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: 2015-10-07
    Changes: Refinement description
  • Version 1.3: 2018-03-14
    Changes: Database references, Source and taxonomy, Structure summary