1I94

CRYSTAL STRUCTURES OF THE SMALL RIBOSOMAL SUBUNIT WITH TETRACYCLINE, EDEINE AND IF3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3.

Pioletti, M.Schlunzen, F.Harms, J.Zarivach, R.Gluhmann, M.Avila, H.Bashan, A.Bartels, H.Auerbach, T.Jacobi, C.Hartsch, T.Yonath, A.Franceschi, F.

(2001) EMBO J 20: 1829-1839

  • DOI: 10.1093/emboj/20.8.1829
  • Primary Citation of Related Structures:  
    1I97, 1I96, 1I95, 1I94

  • PubMed Abstract: 
  • The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3 ...

    The small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. We analyzed by X-ray crystallography the structures of three different complexes of the small ribosomal subunit of Thermus thermophilus with the A-site inhibitor tetracycline, the universal initiation inhibitor edeine and the C-terminal domain of the translation initiation factor IF3. The crystal structure analysis of the complex with tetracycline revealed the functionally important site responsible for the blockage of the A-site. Five additional tetracycline sites resolve most of the controversial biochemical data on the location of tetracycline. The interaction of edeine with the small subunit indicates its role in inhibiting initiation and shows its involvement with P-site tRNA. The location of the C-terminal domain of IF3, at the solvent side of the platform, sheds light on the formation of the initiation complex, and implies that the anti-association activity of IF3 is due to its influence on the conformational dynamics of the small ribosomal subunit.


    Related Citations: 
    • Structure of Functionally Activated Small Ribosomal Subunit at 3.3 A Resolution
      Schluenzen, F., Tocilj, A., Zarivach, R., Harms, J., Gluehmann, M., Janell, D., Bashan, A., Bartels, H., Agmon, I., Franceschi, F., Yonath, A.
      (2000) Cell 102: 615

    Organizational Affiliation

    Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B255Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C238Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D208Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E161Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F101Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G155Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H138Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I128Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S10J104Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K128Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L131Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHN3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13M125Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N60Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P88Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q104Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R87Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S92Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T105Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU26Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAA1514Thermus thermophilus
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download Ideal Coordinates CCD File 
DC [auth A] , DD [auth R] , EC [auth B] , FC [auth B] , GC [auth B] , HC [auth C] , HD [auth T] , LC [auth D] , 
DC [auth A],  DD [auth R],  EC [auth B],  FC [auth B],  GC [auth B],  HC [auth C],  HD [auth T],  LC [auth D],  NC [auth E],  PC [auth G],  QC [auth G],  RC [auth H],  TC [auth J],  VC [auth K]
OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-HWHNUBGVCD
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KC [auth D], ZC [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 P] , BA [auth A] , BB [auth A] , BC [auth A] , BD [auth Q] , 
AA [auth A],  AB [auth A],  AC [auth A],  AD [auth P],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth Q],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth Q],  DA [auth A],  DB [auth A],  EA [auth A],  EB [auth A],  ED [auth T],  FA [auth A],  FB [auth A],  FD [auth T],  GA [auth A],  GB [auth A],  GD [auth T],  HA [auth A],  HB [auth A],  IA [auth A],  IB [auth A],  IC [auth D],  JA [auth A],  JB [auth A],  JC [auth D],  KA [auth A],  KB [auth A],  LA [auth A],  LB [auth A],  MA [auth A],  MB [auth A],  MC [auth E],  NA [auth A],  NB [auth A],  OA [auth A],  OB [auth A],  OC [auth G],  PA [auth A],  PB [auth A],  QA [auth A],  QB [auth A],  RA [auth A],  RB [auth A],  SA [auth A],  SB [auth A],  SC [auth J],  TA [auth A],  TB [auth A],  UA [auth A],  UB [auth A],  UC [auth K],  V [auth A],  VA [auth A],  VB [auth A],  W [auth A],  WA [auth A],  WB [auth A],  WC [auth L],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth L],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth L],  Z [auth A],  ZA [auth A],  ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 406.3α = 90
b = 406.3β = 90
c = 173.1γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance