4DR6

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A structural basis for streptomycin-induced misreading of the genetic code.

Demirci, H.Murphy, F.Murphy, E.Gregory, S.T.Dahlberg, A.E.Jogl, G.

(2013) Nat Commun 4: 1355-1355

  • DOI: 10.1038/ncomms2346
  • Primary Citation of Related Structures:  
    4DR2, 4DR3, 4DR4, 4DR5, 4DR6, 4DR7, 4DR1

  • PubMed Abstract: 
  • During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition ...

    During protein synthesis, the ribosome selects aminoacyl-transfer RNAs with anticodons matching the messenger RNA codon present in the A site of the small ribosomal subunit. The aminoglycoside antibiotic streptomycin disrupts decoding by binding close to the site of codon recognition. Here we use X-ray crystallography to define the impact of streptomycin on the decoding site of the Thermus thermophilus 30S ribosomal subunit in complexes with cognate or near-cognate anticodon stem-loop analogues and messenger RNA. Our crystal structures display a significant local distortion of 16S ribosomal RNA induced by streptomycin, including the crucial bases A1492 and A1493 that participate directly in codon recognition. Consistent with kinetic data, we observe that streptomycin stabilizes the near-cognate anticodon stem-loop analogue complex, while destabilizing the cognate anticodon stem-loop analogue complex. These data reveal how streptomycin disrupts the recognition of cognate anticodon stem-loop analogues and yet improves recognition of a near-cognate anticodon stem-loop analogue.


    Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
UniProt
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14N61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein THXU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1522Thermus thermophilus HB8
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    5'-R(*UP*UP*UP*U)-3'V4Thermus thermophilus HB8
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      5'-R(P*UP*UP*GP*AP*GP*GP*(PSU)P*GP*G)-3'W9Thermus thermophilus HB8
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      • Entity ID: 24
        MoleculeChainsLengthOrganismImage
        5'-R(P*CP*UP*UP*GP*AP*GP*GP*(PSU)P*GP*GP*U)-3'X [auth a]11Thermus thermophilus HB8
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        • Entity ID: 25
          MoleculeChainsLengthOrganismImage
          5'-R(*UP*UP*U)-3'Y [auth b]3Thermus thermophilus HB8
          Protein Feature View
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          • Reference Sequence
          Small Molecules
          Ligands 3 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          SRY
          Query on SRY

          Download Ideal Coordinates CCD File 
          QN [auth A]STREPTOMYCIN
          C21 H39 N7 O12
          UCSJYZPVAKXKNQ-HZYVHMACSA-N
           Ligand Interaction
          ZN
          Query on ZN

          Download Ideal Coordinates CCD File 
          EO [auth N], RN [auth D]ZINC ION
          Zn
          PTFCDOFLOPIGGS-UHFFFAOYSA-N
           Ligand Interaction
          MG
          Query on MG

          Download Ideal Coordinates CCD File 
          AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , 
          AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  AF [auth A],  AG [auth A],  AH [auth A],  AI [auth A],  AJ [auth A],  AK [auth A],  AL [auth A],  AM [auth A],  AN [auth A],  AO [auth G],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  BF [auth A],  BG [auth A],  BH [auth A],  BI [auth A],  BJ [auth A],  BK [auth A],  BL [auth A],  BM [auth A],  BN [auth A],  BO [auth H],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  CF [auth A],  CG [auth A],  CH [auth A],  CI [auth A],  CJ [auth A],  CK [auth A],  CL [auth A],  CM [auth A],  CN [auth A],  CO [auth J],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  DF [auth A],  DG [auth A],  DH [auth A],  DI [auth A],  DJ [auth A],  DK [auth A],  DL [auth A],  DM [auth A],  DN [auth A],  DO [auth L],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  EF [auth A],  EG [auth A],  EH [auth A],  EI [auth A],  EJ [auth A],  EK [auth A],  EL [auth A],  EM [auth A],  EN [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  FF [auth A],  FG [auth A],  FH [auth A],  FI [auth A],  FJ [auth A],  FK [auth A],  FL [auth A],  FM [auth A],  FN [auth A],  FO [auth N],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  GF [auth A],  GG [auth A],  GH [auth A],  GI [auth A],  GJ [auth A],  GK [auth A],  GL [auth A],  GM [auth A],  GN [auth A],  GO [auth P],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  HF [auth A],  HG [auth A],  HH [auth A],  HI [auth A],  HJ [auth A],  HK [auth A],  HL [auth A],  HM [auth A],  HN [auth A],  HO [auth P],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  IF [auth A],  IG [auth A],  IH [auth A],  II [auth A],  IJ [auth A],  IK [auth A],  IL [auth A],  IM [auth A],  IN [auth A],  IO [auth P],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  JF [auth A],  JG [auth A],  JH [auth A],  JI [auth A],  JJ [auth A],  JK [auth A],  JL [auth A],  JM [auth A],  JN [auth A],  JO [auth Q],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  KF [auth A],  KG [auth A],  KH [auth A],  KI [auth A],  KJ [auth A],  KK [auth A],  KL [auth A],  KM [auth A],  KN [auth A],  KO [auth S],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  LF [auth A],  LG [auth A],  LH [auth A],  LI [auth A],  LJ [auth A],  LK [auth A],  LL [auth A],  LM [auth A],  LN [auth A],  LO [auth S],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  MF [auth A],  MG [auth A],  MH [auth A],  MI [auth A],  MJ [auth A],  MK [auth A],  ML [auth A],  MM [auth A],  MN [auth A],  MO [auth S],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  NF [auth A],  NG [auth A],  NH [auth A],  NI [auth A],  NJ [auth A],  NK [auth A],  NL [auth A],  NM [auth A],  NN [auth A],  NO [auth T],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  OF [auth A],  OG [auth A],  OH [auth A],  OI [auth A],  OJ [auth A],  OK [auth A],  OL [auth A],  OM [auth A],  ON [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth A],  PF [auth A],  PG [auth A],  PH [auth A],  PI [auth A],  PJ [auth A],  PK [auth A],  PL [auth A],  PM [auth A],  PN [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth A],  QF [auth A],  QG [auth A],  QH [auth A],  QI [auth A],  QJ [auth A],  QK [auth A],  QL [auth A],  QM [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth A],  RF [auth A],  RG [auth A],  RH [auth A],  RI [auth A],  RJ [auth A],  RK [auth A],  RL [auth A],  RM [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  SE [auth A],  SF [auth A],  SG [auth A],  SH [auth A],  SI [auth A],  SJ [auth A],  SK [auth A],  SL [auth A],  SM [auth A],  SN [auth D],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth A],  TF [auth A],  TG [auth A],  TH [auth A],  TI [auth A],  TJ [auth A],  TK [auth A],  TL [auth A],  TM [auth A],  TN [auth D],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth A],  UF [auth A],  UG [auth A],  UH [auth A],  UI [auth A],  UJ [auth A],  UK [auth A],  UL [auth A],  UM [auth A],  UN [auth D],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  VE [auth A],  VF [auth A],  VG [auth A],  VH [auth A],  VI [auth A],  VJ [auth A],  VK [auth A],  VL [auth A],  VM [auth A],  VN [auth E],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  WE [auth A],  WF [auth A],  WG [auth A],  WH [auth A],  WI [auth A],  WJ [auth A],  WK [auth A],  WL [auth A],  WM [auth A],  WN [auth E],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  XE [auth A],  XF [auth A],  XG [auth A],  XH [auth A],  XI [auth A],  XJ [auth A],  XK [auth A],  XL [auth A],  XM [auth A],  XN [auth E],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  YE [auth A],  YF [auth A],  YG [auth A],  YH [auth A],  YI [auth A],  YJ [auth A],  YK [auth A],  YL [auth A],  YM [auth A],  YN [auth F],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A],  ZE [auth A],  ZF [auth A],  ZG [auth A],  ZH [auth A],  ZI [auth A],  ZJ [auth A],  ZK [auth A],  ZL [auth A],  ZM [auth A],  ZN [auth F]
          MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          Modified Residues  1 Unique
          IDChainsTypeFormula2D DiagramParent
          0TD
          Query on 0TD
          LL-PEPTIDE LINKINGC5 H9 N O4 SASP
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 3.30 Å
          • R-Value Free: 0.192 
          • R-Value Work: 0.153 
          • R-Value Observed: 0.155 
          • Space Group: P 41 21 2
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 402.6α = 90
          b = 402.6β = 90
          c = 174.9γ = 90
          Software Package:
          Software NamePurpose
          XSCALEdata scaling
          PHENIXrefinement
          PDB_EXTRACTdata extraction
          HKL-2000data collection
          XDSdata reduction
          PHENIXphasing

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History  (Full details and data files)

          • Version 1.0: 2012-11-14
            Type: Initial release
          • Version 1.1: 2013-01-23
            Changes: Database references
          • Version 1.2: 2013-01-30
            Changes: Database references