1FKA

STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.304 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of functionally activated small ribosomal subunit at 3.3 angstroms 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: 615-623

  • DOI: 10.1016/s0092-8674(00)00084-2
  • Primary Citation of Related Structures:  
    1FKA

  • PubMed Abstract: 
  • The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The ent ...

    The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle's far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation.


    Related Citations: 
    • Refining the overall structure and subdomain orientation of ribosomal protein S4 delta 41 with dipolar couplings measured by nmr in uniaxial liquid crystalline phases
      MARKUS, M.A., GERSTNER, R.B., DRAPER, D.E., Torchia, D.A.
      (1999) J Mol Biol 292: 375
    • The structure of ribosomal protein s5 reveals sites of interaction with 16S rRNA
      RAMAKRISHNAN, V., WHITE, S.W.
      (1992) Nature 358: 768
    • Crystal structure of the ribosomal protein S6 from Thermus thermophilus
      LINDAHL, M., SVENSSON, L.A., LILJAS, A., SEDELNIKOVA, S.E., ELISEIKINA, I.A., FOMENKOVA, N.P., NEVSKAYA, N., NIKONOV, S.V., GARBER, M.B., MURANOVA, T.A., RYKONOVA, A.I.
      (1994) EMBO J 13: 1249
    • The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids
      WIMBERLY, B.T., WHITE, S.W., RAMAKRISHNAN, V.
      (1997) Structure 15: 1187
    • Crystal structure of ribosomal protein S8 from Thermus thermophilus reveals a high degree of structural conservation of a specific RNA binding site
      NEVSKAYA, N., TISHCHENKO, S., NIKULIN, A., AL-KARADAGHI, S., LILJAS, A., EHRESMANN, B., EHRESMANN, C., GARBER, M.B., NIKONOV, S.
      (1998) J Mol Biol 279: 233
    • Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
      CLEMONS, W.M., DAVIES, C., WHITE, S.W., RAMAKRISHNAN, V.
      (1998) Structure 6: 429
    • Structure of the S15, S6, S18-rRNA complex: assembly of the 30S ribosome central domain
      AGALAROV, S.C., PRASAD, G.S., FUNKE, P.M., STOUT, C.D., WILLIAMSON, J.R.
      (2000) Science 288: 107
    • Solution structure of the ribosomal protein S19 from Thermus thermophilus
      HELGSTRAND, M., RAK, A.V., ALLARD, P., DAVYDOVA, N., GARBER, M.B., HARD, T.
      (1999) J Mol Biol 292: 1071

    Organizational Affiliation

    Max-Planck-Research Unit for Ribosomal Structure, Hamburg, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B111Thermus thermophilusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C176Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D209Thermus thermophilusMutation(s): 0 
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E162Thermus thermophilusMutation(s): 0 
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 thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G151Thermus thermophilusMutation(s): 0 
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 thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I89Thermus thermophilusMutation(s): 0 
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S10J71Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11K70Thermus thermophilusMutation(s): 0 
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S12L103Thermus thermophilusMutation(s): 0 
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13M77Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N26Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O89Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P73Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q84Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S93Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T95Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1518Thermus thermophilus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download CCD File 
A, C, G, H, K, R
OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-HWHNUBGVCD
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.304 
  • 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 

  • Version 1.0: 2000-09-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance