4X65

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics.

Choi, J.Ieong, K.W.Demirci, H.Chen, J.Petrov, A.Prabhakar, A.O'Leary, S.E.Dominissini, D.Rechavi, G.Soltis, S.M.Ehrenberg, M.Puglisi, J.D.

(2016) Nat Struct Mol Biol 23: 110-115

  • DOI: 10.1038/nsmb.3148
  • Primary Citation of Related Structures:  
    4X62, 4X64, 4X65, 4X66

  • PubMed Abstract: 
  • N(6)-methylation of adenosine (forming m(6)A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)A in mRNA decoding ...

    N(6)-methylation of adenosine (forming m(6)A) is the most abundant post-transcriptional modification within the coding region of mRNA, but its role during translation remains unknown. Here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)A in mRNA decoding. Although m(6)A base-pairs with uridine during decoding, as shown by X-ray crystallographic analyses of Thermus thermophilus ribosomal complexes, our measurements in an Escherichia coli translation system revealed that m(6)A modification of mRNA acts as a barrier to tRNA accommodation and translation elongation. The interaction between an m(6)A-modified codon and cognate tRNA echoes the interaction between a near-cognate codon and tRNA, because delay in tRNA accommodation depends on the position and context of m(6)A within codons and on the accuracy level of translation. Overall, our results demonstrate that chemical modification of mRNA can change translational dynamics.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California, USA.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B236Thermus 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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E151Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G155Thermus 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 LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN60Thermus 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 LengthOrganismDetailsImage
30S ribosomal protein S15O88Thermus 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 LengthOrganismDetailsImage
30S ribosomal protein S16P84Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S81Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxU25Thermus 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
    RNA (5'-D(*AP*(MA6)P*AP*UP*UP*U)-3')V [auth a]6Thermus thermophilus HB8
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      RNA (5'-D(P*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*C)-3')W [auth b]11Thermus thermophilus HB8
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PAR
      Query on PAR

      Download Ideal Coordinates CCD File 
      AA [auth A], BA [auth A], CA [auth A], X [auth A], Y [auth A], Z [auth A]PAROMOMYCIN
      C23 H45 N5 O14
      UOZODPSAJZTQNH-LSWIJEOBSA-N
       Ligand Interaction
      ZN
      Query on ZN

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      FN [auth D], RN [auth N]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

      Download Ideal Coordinates CCD File 
      AM [auth A] , AN [auth A] , BM [auth A] , BN [auth A] , CM [auth A] , DM [auth A] , EM [auth A] , FM [auth A] , 
      AM [auth A],  AN [auth A],  BM [auth A],  BN [auth A],  CM [auth A],  DM [auth A],  EM [auth A],  FM [auth A],  GM [auth A],  HM [auth A],  IM [auth A],  IN [auth E],  JM [auth A],  KL [auth A],  KM [auth A],  LL [auth A],  LM [auth A],  ML [auth A],  MM [auth A],  MN [auth G],  NL [auth A],  NM [auth A],  OL [auth A],  OM [auth A],  PL [auth A],  PM [auth A],  QL [auth A],  QM [auth A],  RL [auth A],  RM [auth A],  SL [auth A],  SM [auth A],  TL [auth A],  TM [auth A],  UL [auth A],  UM [auth A],  VL [auth A],  VM [auth A],  WL [auth A],  WM [auth A],  XL [auth A],  XM [auth A],  YL [auth A],  YM [auth A],  ZL [auth A],  ZM [auth A]
      POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , AF [auth A] , AG [auth A] , AH [auth A] , AI [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],  AO [auth S],  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],  BO [auth S],  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],  CN [auth A],  CO [auth T],  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],  DN [auth A],  DO [auth b],  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],  EN [auth C],  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],  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],  GN [auth D],  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],  HN [auth E],  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],  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],  JN [auth F],  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],  KN [auth G],  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],  LN [auth G],  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],  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],  NN [auth H],  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],  ON [auth H],  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],  PN [auth L],  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],  QN [auth L],  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],  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],  SN [auth P],  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],  TN [auth P],  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],  UN [auth P],  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],  VN [auth P],  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],  WN [auth Q],  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],  XN [auth Q],  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],  YN [auth Q],  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],  ZN [auth S]
      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: 3.35 Å
      • R-Value Free: 0.210 
      • R-Value Work: 0.184 
      • R-Value Observed: 0.185 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 401.44α = 90
      b = 401.44β = 90
      c = 175.924γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      PDB_EXTRACTdata extraction
      PHENIXphasing

      Structure Validation

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      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM51266
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099687

      Revision History  (Full details and data files)

      • Version 1.0: 2015-11-18
        Type: Initial release
      • Version 1.1: 2016-01-13
        Changes: Database references
      • Version 1.2: 2016-01-27
        Changes: Database references
      • Version 1.3: 2016-02-10
        Changes: Database references
      • Version 1.4: 2017-09-06
        Changes: Author supporting evidence, Derived calculations
      • Version 2.0: 2019-12-25
        Changes: Author supporting evidence, Polymer sequence