4WQF

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G and fusidic acid in the post-translocational state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report



Literature

Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation.

Lin, J.Gagnon, M.G.Bulkley, D.Steitz, T.A.

(2015) Cell 160: 219-227

  • DOI: 10.1016/j.cell.2014.11.049
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements dur ...

    The universally conserved GTPase elongation factor G (EF-G) catalyzes the translocation of tRNA and mRNA on the ribosome after peptide bond formation. Despite numerous studies suggesting that EF-G undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of EF-G in complex with the ribosome. Here, we report four atomic-resolution crystal structures of EF-G bound to the ribosome programmed in the pre- and posttranslocational states and to the ribosome trapped by the antibiotic dityromycin. We observe a previously unseen conformation of EF-G in the pretranslocation complex, which is independently captured by dityromycin on the ribosome. Our structures provide insights into the conformational space that EF-G samples on the ribosome and reveal that tRNA translocation on the ribosome is facilitated by a structural transition of EF-G from a compact to an elongated conformation, which can be prevented by the antibiotic dityromycin.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA; Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA. Electronic address: thomas.steitz@yale.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
AC, CC
228Thermus thermophilusMutation(s): 0 
Gene Names: rplATTHA0246
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
AD, CD
276Thermus thermophilusMutation(s): 0 
Gene Names: rplBTTHA1689
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
AE, CE
206Thermus thermophilusMutation(s): 0 
Gene Names: rplCTTHA1692
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
AF, CF
210Thermus thermophilusMutation(s): 0 
Gene Names: rplDTTHA1691
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
AG, CG
182Thermus thermophilusMutation(s): 0 
Gene Names: rplETTHA1680
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
AH, CH
180Thermus thermophilusMutation(s): 0 
Gene Names: rplFTTHA1677
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
AK, CK
173Thermus thermophilusMutation(s): 0 
Gene Names: rplJTTHA0209
Find proteins for Q8VVE3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
AL, CL
147Thermus thermophilusMutation(s): 0 
Gene Names: rplKTTHA0247
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
AN, CN
140Thermus thermophilusMutation(s): 0 
Gene Names: rplMTTHA1465
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
AO, CO
122Thermus thermophilusMutation(s): 0 
Gene Names: rplNTTHA1682
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
AP, CP
150Thermus thermophilusMutation(s): 0 
Gene Names: rplOTTHA1673
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
AQ, CQ
141Thermus thermophilusMutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
AR, CR
118Thermus thermophilusMutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
AS, CS
112Thermus thermophilusMutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
AT, CT
146Thermus thermophilusMutation(s): 0 
Gene Names: rplSTTHA1031
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
AU, CU
118Thermus thermophilusMutation(s): 0 
Gene Names: rplTTTHA0553
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
AV, CV
101Thermus thermophilusMutation(s): 0 
Gene Names: rplUTTHA1783
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
AW, CW
113Thermus thermophilusMutation(s): 0 
Gene Names: rplVTTHA1687
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
AX, CX
96Thermus thermophilusMutation(s): 0 
Gene Names: rplWTTHA1690
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
AY, CY
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
AZ, CZ
206Thermus thermophilusMutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
A0, C0
85Thermus thermophilusMutation(s): 0 
Gene Names: rpmATTHA1782
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
A1, C1
98Thermus thermophilusMutation(s): 0 
Gene Names: rpmBTTHA0042
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
A2, C2
72Thermus thermophilusMutation(s): 0 
Gene Names: rpmCTTHA1684
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
A3, C3
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmDTTHA1674
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
A4, C4
71Thermus thermophilusMutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
A5, C5
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
A6, C6
54Thermus thermophilusMutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
A7, C7
49Thermus thermophilusMutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
A8, C8
65Thermus thermophilusMutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
A9, C9
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJTTHA1668
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR2

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
BB, DB
256Thermus thermophilusMutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
BC, DC
239Thermus thermophilusMutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
BD, DD
209Thermus thermophilusMutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
BE, DE
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
BF, DF
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
BG, DG
156Thermus thermophilusMutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
BH, DH
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
BI, DI
128Thermus thermophilusMutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
BJ, DJ
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
BK, DK
129Thermus thermophilusMutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BL, DL
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
BM, DM
126Thermus thermophilusMutation(s): 0 
Gene Names: rpsMrps13TTHA1667
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
BN, DN
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
BO, DO
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
BP, DP
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
BQ, DQ
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
BR, DR
88Thermus thermophilusMutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
BS, DS
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
BT, DT
106Thermus thermophilusMutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
BU, DU
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9,Elongation factor G
BZ, DZ
758Thermus thermophilusMutation(s): 0 
Gene Names: rplITTHA0242
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Find proteins for Q5SHN5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN5

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Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNAAA, CA2915Thermus thermophilus HB8

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Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNAAB, CB121Thermus thermophilus HB8

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Entity ID: 34
MoleculeChainsLengthOrganism
16S Ribosomal RNABA, DA1521Thermus thermophilus HB8
Entity ID: 55
MoleculeChainsLengthOrganism
mRNABV, DV18synthetic construct

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Entity ID: 56
MoleculeChainsLengthOrganism
P-site tRNABW, BY,DW,DY76Escherichia coli str. K-12 substr. MC4100
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUA
Query on FUA

Download CCD File 
BZ, DZ
FUSIDIC ACID
C31 H48 O6
IECPWNUMDGFDKC-MZJAQBGESA-N
 Ligand Interaction
GDP
Query on GDP

Download CCD File 
BZ, DZ
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
BD, DD
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A4, A5, A6, A9, AY, BN, C4, C5, C6, C9, CY, DN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A0, A2, A4, A5, A6, A7, A8, A9, AA, AB, AD, AE, AF, AG, AH, AN, AO, AP, AQ, AR, AU, AV, AW, AX, AY, AZ, BA, BB, BD, BE, BF, BK, BL, BM, BN, BT, BV, BW, BZ, C3, C5, C7, C8, CA, CB, CD, CE, CF, CG, CN, CO, CP, CQ, CR, CU, CV, CW, CY, DA, DD, DE, DF, DJ, DK, DT, DW, DZ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.446α = 90
b = 449.005β = 90
c = 625.366γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Advisory, Derived calculations, Refinement description, Source and taxonomy
  • Version 2.0: 2019-07-03
    Changes: Data collection, Non-polymer description, Structure summary