5WNT

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

  • Classification: RIBOSOME
  • Organism(s): Thermus thermophilus HB8
  • Mutation(s): No 

  • Deposited: 2017-08-01 Released: 2018-02-21 
  • Deposition Author(s): DeMirci, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation.

Choi, J.Indrisiunaite, G.DeMirci, H.Ieong, K.W.Wang, J.Petrov, A.Prabhakar, A.Rechavi, G.Dominissini, D.He, C.Ehrenberg, M.Puglisi, J.D.

(2018) Nat Struct Mol Biol 25: 208-216

  • DOI: 10.1038/s41594-018-0030-z
  • Primary Citation of Related Structures:  
    5WNU, 5WNT, 5WNV, 5WNQ, 5WNP, 5WNS, 5WNR

  • PubMed Abstract: 
  • Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids ...

    Chemical modifications of mRNA may regulate many aspects of mRNA processing and protein synthesis. Recently, 2'-O-methylation of nucleotides was identified as a frequent modification in translated regions of human mRNA, showing enrichment in codons for certain amino acids. Here, using single-molecule, bulk kinetics and structural methods, we show that 2'-O-methylation within coding regions of mRNA disrupts key steps in codon reading during cognate tRNA selection. Our results suggest that 2'-O-methylation sterically perturbs interactions of ribosomal-monitoring bases (G530, A1492 and A1493) with cognate codon-anticodon helices, thereby inhibiting downstream GTP hydrolysis by elongation factor Tu (EF-Tu) and A-site tRNA accommodation, leading to excessive rejection of cognate aminoacylated tRNAs in initial selection and proofreading. Our current and prior findings highlight how chemical modifications of mRNA tune the dynamics of protein synthesis at different steps of translation elongation.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. puglisi@stanford.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S2 B236Thermus 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
RIBOSOMAL PROTEIN S3 C207Thermus 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
RIBOSOMAL PROTEIN S4 D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S5 E151Thermus 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
RIBOSOMAL PROTEIN S6 F101Thermus 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 LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S7 G155Thermus 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
RIBOSOMAL PROTEIN S8 H138Thermus 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
RIBOSOMAL PROTEIN S9 I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S10 J99Thermus 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 LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S11 K119Thermus 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 LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S12 L125Thermus 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 LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S13 M118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S14 N60Thermus 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
RIBOSOMAL PROTEIN S15 O88Thermus 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
RIBOSOMAL PROTEIN S16 P84Thermus 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
RIBOSOMAL PROTEIN S17 Q99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S18 R73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S19 S81Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S20 T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN THX U25Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S Ribosomal RNA rRNAA1522Thermus thermophilus HB8
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*(A2M)P*AP*AP*UP*U)-3')a5Thermus thermophilus HB8
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      RNA (5'-R(P*UP*AP*GP*AP*CP*UP*(70U)P*UP*UP*(12A)P*AP*(PSU)P*CP*UP*A)-3')b15Thermus thermophilus HB8
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      B6M
      Query on B6M

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      A
      (1R,2S,3S,4R,6R)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-alpha-L-altropyranosyl)-beta-L-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-allopyranoside
      C23 H45 N5 O14
      UOZODPSAJZTQNH-JMVAARTISA-N
       Ligand Interaction
      ZN
      Query on ZN

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      D, N
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

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      A
      POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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      A, D, E, F, G, H, L, P, Q, S, T
      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: 0.212 
      • R-Value Work: 0.173 
      • R-Value Observed: 0.173 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 400α = 90
      b = 400β = 90
      c = 173γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XSCALEdata scaling
      PDB_EXTRACTdata extraction
      XDSdata reduction
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data

      • Deposited Date: 2017-08-01 
      • Released Date: 2018-02-21 
      • Deposition Author(s): DeMirci, H.

      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM51266 and GM099687

      Revision History  (Full details and data files)

      • Version 1.0: 2018-02-21
        Type: Initial release
      • Version 1.1: 2018-02-28
        Changes: Author supporting evidence
      • Version 1.2: 2018-03-07
        Changes: Database references
      • Version 1.3: 2018-03-14
        Changes: Database references, Structure summary
      • Version 2.0: 2018-03-21
        Changes: Polymer sequence, Source and taxonomy, Structure summary
      • Version 2.1: 2020-01-01
        Changes: Author supporting evidence
      • Version 2.2: 2020-10-21
        Changes: Data collection, Derived calculations