1QD7

PARTIAL MODEL FOR 30S RIBOSOMAL SUBUNIT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 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

  • 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
    • Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy
      Jaishree, T.N.,Ramakrishnan, V.,White, S.W.
      (1996) Biochemistry 35: 2845
    • 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
    • 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 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
    • 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
    • The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA
      Ramakrishnan, V.,White, S.W.
      (1992) Nature 358: 768


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
S4 RIBOSOMAL PROTEIN
C
159Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rpsD
Find proteins for P81288 (Geobacillus stearothermophilus)
Go to UniProtKB:  P81288
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
S5 RIBOSOMAL PROTEIN
D
145Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rpsE
Find proteins for P02357 (Geobacillus stearothermophilus)
Go to UniProtKB:  P02357
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
S6 RIBOSOMAL PROTEIN
E
97Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
S7 RIBOSOMAL PROTEIN
F
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
S8 RIBOSOMAL PROTEIN
G
136Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
S15 RIBOSOMAL PROTEIN
H
85Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rpsO
Find proteins for P05766 (Geobacillus stearothermophilus)
Go to UniProtKB:  P05766
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
S17 RIBOSOMAL PROTEIN
I
89Geobacillus stearothermophilusMutation(s): 0 
Gene Names: rpsQ
Find proteins for P23828 (Geobacillus stearothermophilus)
Go to UniProtKB:  P23828
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
S20 RIBOSOMAL PROTEIN
J
100N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
CENTRAL FRAGMENT OF 16 S RNAA271Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
END FRAGMENT OF 16 S RNAB88Thermus thermophilus
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
J
L-PEPTIDE LINKINGC4 H9 N O2

--

N
Query on N
A, B
RNA LINKINGC5 H11 O7 P

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 401.600α = 90.00
b = 401.600β = 90.00
c = 174.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SOLVEphasing
SCALEPACKdata scaling
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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