1J5E

Structure of the Thermus thermophilus 30S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the 30S ribosomal subunit.

Wimberly, B.T.Brodersen, D.E.Clemons Jr., W.M.Morgan-Warren, R.J.Carter, A.P.Vonrhein, C.Hartsch, T.Ramakrishnan, V.

(2000) Nature 407: 327-339

  • DOI: 10.1038/35030006
  • Also Cited By: 1X18, 1T1O, 1T1M

  • PubMed Abstract: 
  • Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from The ...

    Genetic information encoded in messenger RNA is translated into protein by the ribosome, which is a large nucleoprotein complex comprising two subunits, denoted 30S and 50S in bacteria. Here we report the crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 A resolution. The final atomic model rationalizes over four decades of biochemical data on the ribosome, and provides a wealth of information about RNA and protein structure, protein-RNA interactions and ribosome assembly. It is also a structural basis for analysis of the functions of the 30S subunit, such as decoding, and for understanding the action of antibiotics. The structure will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.


    Related Citations: 
    • Structure of a Bacterial 30S Ribosomal Subunit at 5.5 A Resolution
      Clemons Jr., W.M.,May, J.L.C.,Wimberly, B.T.,McCutcheon, J.P.,Capel, M.S.,Ramakrishnan, V.
      (1999) Nature 400: 833
    • 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, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
B
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
C
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
D
208Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
E
161Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
F
101Thermus 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: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
G
155Thermus 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: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
H
138Thermus aquaticusMutation(s): 0 
Gene Names: rpsH
Find proteins for A0A0M9AFS9 (Thermus aquaticus)
Go to UniProtKB:  A0A0M9AFS9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
I
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
J
104Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
K
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
L
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
M
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
N
60Thermus aquaticusMutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for A0A0N0BLP2 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLP2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
O
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
P
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
Q
104Thermus aquaticusMutation(s): 0 
Gene Names: rpsQ
Find proteins for A0A0N0BLS5 (Thermus aquaticus)
Go to UniProtKB:  A0A0N0BLS5
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
R
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
S
92Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
T
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
V
26Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAA1522Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, N
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A, B, M
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 401.375α = 90.00
b = 401.375β = 90.00
c = 175.887γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-12
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance