1QD7

PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a bacterial 30S ribosomal subunit at 5.5 A resolution.

Clemons Jr., W.M.May, J.L.Wimberly, B.T.McCutcheon, J.P.Capel, M.S.Ramakrishnan, V.

(1999) Nature 400: 833-840

  • DOI: 10.1038/23631
  • Primary Citation of Related Structures:  
    1QD7

  • PubMed Abstract: 
  • The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5 ...

    The 30S ribosomal subunit binds messenger RNA and the anticodon stem-loop of transfer RNA during protein synthesis. A crystallographic analysis of the structure of the subunit from the bacterium Thermus thermophilus is presented. At a resolution of 5.5 A, the phosphate backbone of the ribosomal RNA is visible, as are the alpha-helices of the ribosomal proteins, enabling double-helical regions of RNA to be identified throughout the subunit, all seven of the small-subunit proteins of known crystal structure to be positioned in the electron density map, and the fold of the entire central domain of the small-subunit ribosomal RNA to be determined.


    Related Citations: 
    • The crystal structure of ribosomal protein S4 reveals a two-domain molecule with an extensive RNA-binding surface: one domain shows structural homology to the ETS DNA-binding motif
      Davies, C., Gerstner, R.B., Draper, D.E., Ramakrishnan, V., White, S.W.
      (1998) EMBO J 17: 4545
    • 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, I.A., Eliseikina, I.A., Fomenkova, N.P., Nevskaya, N., Nikonov, S.V., Garber, M.B., Muranova, T.A., Rykonova, A.I., Amons, R.
      (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 5: 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., Tischenko, S., Nikulin, A., Al-Karadaghi, S., Liljas, A., Ehresmann, B., Ehresmann, C., Garber, M., Nikonov, S.
      (1998) J Mol Biol 279: 233
    • Conformational variability of the N-terminal helix in the structure of ribosomal protein S15
      Clemons Jr., W.M., Davies, C.R., White, S.W., Ramakrishnan, V.
      (1998) Structure 6: 429
    • Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy
      Jaishree, T.N., Ramakrishnan, V., White, S.W.
      (1996) Biochemistry 35: 2845

    Organizational Affiliation

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City 84103, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
S4 RIBOSOMAL PROTEINC159Thermus thermophilusMutation(s): 0 
Find proteins for P81288 (Geobacillus stearothermophilus)
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Go to UniProtKB:  P81288
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
S5 RIBOSOMAL PROTEIND145Thermus thermophilusMutation(s): 0 
Find proteins for P02357 (Geobacillus stearothermophilus)
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Go to UniProtKB:  P02357
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
S6 RIBOSOMAL PROTEINE97Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SLP8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
S7 RIBOSOMAL PROTEINF135Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  P17291
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
S8 RIBOSOMAL PROTEING136Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  P0DOY9
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
S15 RIBOSOMAL PROTEINH85Thermus thermophilusMutation(s): 0 
Find proteins for P05766 (Geobacillus stearothermophilus)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
S17 RIBOSOMAL PROTEINI89Thermus thermophilusMutation(s): 0 
Find proteins for P23828 (Geobacillus stearothermophilus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
S20 RIBOSOMAL PROTEINJ100Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
CENTRAL FRAGMENT OF 16 S RNAA271Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
END FRAGMENT OF 16 S RNAB88Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.6α = 90
b = 401.6β = 90
c = 174.5γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
Omodel building
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance