1IBL

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of cognate transfer RNA by the 30S ribosomal subunit.

Ogle, J.M.Brodersen, D.E.Clemons Jr., W.M.Tarry, M.J.Carter, A.P.Ramakrishnan, V.

(2001) Science 292: 897-902

  • DOI: 10.1126/science.1060612
  • Primary Citation of Related Structures:  
    1IBM, 1IBL, 1IBK

  • PubMed Abstract: 
  • Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA ...

    Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.


    Related Citations: 
    • Structure of the 30S Ribosomal Subunit
      Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R., Carter, A.P., Vonrhein, C., Hartsch, T., Ramakrishnan, V.
      (2000) Nature 407: 327
    • Functional Insights from the Structure of the 30S Ribosomal Subunit and its Interactions with Antibiotics
      Carter, A.P., Clemons Jr., W.M., Brodersen, D.E., Wimberly, B.T., Morgan-Warren, R., Ramakrishnan, V.
      (2000) Nature 407: 340

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2E [auth B]256Thermus thermophilusMutation(s): 0 
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80371 
Go to UniProtKB:  P80371
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3F [auth C]239Thermus thermophilusMutation(s): 0 
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80372 
Go to UniProtKB:  P80372
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4G [auth D]209Thermus thermophilusMutation(s): 0 
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80373 
Go to UniProtKB:  P80373
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5H [auth E]162Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHQ5 
Go to UniProtKB:  Q5SHQ5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6I [auth F]101Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLP8 
Go to UniProtKB:  Q5SLP8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7J [auth G]156Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P17291 
Go to UniProtKB:  P17291
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8K [auth H]138Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY9 
Go to UniProtKB:  P0DOY9
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9L [auth I]128Thermus thermophilusMutation(s): 0 
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80374 
Go to UniProtKB:  P80374
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10M [auth J]105Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHN7 
Go to UniProtKB:  Q5SHN7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11N [auth K]129Thermus thermophilusMutation(s): 0 
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80376 
Go to UniProtKB:  P80376
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12O [auth L]135Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHN3 
Go to UniProtKB:  Q5SHN3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13P [auth M]126Thermus thermophilusMutation(s): 0 
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80377 
Go to UniProtKB:  P80377
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14Q [auth N]61Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY6 
Go to UniProtKB:  P0DOY6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15R [auth O]89Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJ76 
Go to UniProtKB:  Q5SJ76
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16S [auth P]88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJH3 
Go to UniProtKB:  Q5SJH3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17T [auth Q]105Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P0DOY7 
Go to UniProtKB:  P0DOY7
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18U [auth R]88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLQ0 
Go to UniProtKB:  Q5SLQ0
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19V [auth S]93Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHP2 
Go to UniProtKB:  Q5SHP2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20W [auth T]106Thermus thermophilusMutation(s): 0 
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P80380 
Go to UniProtKB:  P80380
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXX [auth V]26Thermus thermophilusMutation(s): 0 
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SIH3 
Go to UniProtKB:  Q5SIH3
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1522Thermus thermophilus
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    P-SITE MESSENGER RNA FRAGMENTB [auth X]6N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      ANTICODON STEM-LOOP OF PHENYLALANINE TRANSFER RNAC [auth Y]15N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        A-SITE MESSENGER RNA FRAGMENTD [auth Z]4N/A
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        PAR
        Query on PAR

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

        Download Ideal Coordinates CCD File 
        SE [auth D], VE [auth N]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] , BA [auth A] , BB [auth A] , BC [auth A] , 
        AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  FE [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  HE [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  IE [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  JE [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  KE [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  LE [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  ME [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  ND [auth A],  NE [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  OE [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  PE [auth Y],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  QE [auth D],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  RE [auth D],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  TE [auth J],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  UE [auth J],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A]
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 3.11 Å
        • R-Value Free: 0.275 
        • R-Value Work: 0.232 
        • Space Group: P 41 21 2
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 400.8α = 90
        b = 400.8β = 90
        c = 175.885γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data collection
        SCALEPACKdata scaling
        CNSrefinement
        HKL-2000data reduction
        CNSphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2001-05-04
          Type: Initial release
        • Version 1.1: 2008-04-27
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance