1VY7

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Cytidine-Puromycin in the A site and acylated tRNA in the P site.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation 3D Report Full Report



Literature

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.

Polikanov, Y.S.Steitz, T.A.Innis, C.A.

(2014) Nat Struct Mol Biol 21: 787-793

  • DOI: 10.1038/nsmb.2871
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During peptide-bond formation on the ribosome, the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly e ...

    During peptide-bond formation on the ribosome, the α-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-Å resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.


    Organizational Affiliation

    1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2].



Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10AJ, CJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11AK, CK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12AL, CL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13AM, CM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type ZAN, CN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15AO, CO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16AP, CP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17AQ, CQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18AR, CR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19AS, CS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2AB, CB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20AT, CT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein ThxAU, CU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2BD, DD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3BE, DE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AC, CC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4BF, DF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5BG, DG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6BH, DH180Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0M9ADP1 (Thermus aquaticus)
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9BI, DI148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13BN, DN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14BO, DO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15BP, DP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16BQ, DQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17BR, DR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18BS, DS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4AD, CD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19BT, DT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20BU, DU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21BV, DV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22BW, DW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23BX, DX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24BY, DY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25BZ, DZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27B0, D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28B1, D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29B2, D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5AE, CE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30B3, D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31B4, D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32B5, D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33B6, D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34B7, D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35B8, D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36B9, D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6AF, CF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7AG, CG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8AH, CH138Thermus thermophilus HB8Mutation(s): 0 
Find proteins for A0A0M9AFS9 (Thermus aquaticus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9AI, CI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 1
MoleculeChainsLengthOrganism
16S Ribosomal RNAAA, CA1521Thermus thermophilus HB8

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Entity ID: 22
MoleculeChainsLengthOrganism
mRNAAV, CV24synthetic construct
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Entity ID: 23
MoleculeChainsLengthOrganism
Cytidine-PuromycinAW, CW3synthetic construct

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Entity ID: 24
MoleculeChainsLengthOrganism
P-site tRNAAX, CX77Escherichia coli

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Entity ID: 25
MoleculeChainsLengthOrganism
E-site tRNAAY, CY76Escherichia coli

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Entity ID: 26
MoleculeChainsLengthOrganism
23S Ribosomal RNABA, DA2915Thermus thermophilus HB8

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Entity ID: 27
MoleculeChainsLengthOrganism
5S Ribosomal RNABB, DB121Thermus thermophilus HB8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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AD, CD
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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AN, B4, B5, B6, B9, BY, CN, D4, D5, D6, D9, DY
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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AX, CX
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, AD, AE, AF, AJ, AK, AM, AN, AS, AV, AW, AX, B0, B1, B2, B3, B5, B7, B8, B9, BA, BB, BD, BE, BF, BG, BN, BO, BP, BQ, BR, BU, BV, BW, BX, BY, BZ, CA, CE, CF, CJ, CK, CT, CW, CX, D3, D5, D8, DA, DB, DD, DE, DF, DG, DN, DO, DP, DQ, DR, DU, DV, DW, DY
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.56α = 90
b = 444.23β = 90
c = 613.03γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-09-17
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2014-12-17
    Changes: Other
  • Version 1.5: 2015-01-28
    Changes: Other
  • Version 2.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary