1I94

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 

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:  

  • 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 su ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
B
255Thermus 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
238Thermus 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 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: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
I
128Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
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
128Thermus 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
131Thermus 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
125Thermus 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
87Thermus 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
105Thermus 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
U
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 RRNAA1514Thermus thermophilus
Small Molecules
Ligands 3 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
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, E, G, J, K, L, P, Q, T
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
WO2
Query on WO2

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 406.300α = 90.00
b = 406.300β = 90.00
c = 173.100γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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