1I97

CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH TETRACYCLINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1093/emboj/20.8.1829
  • Primary Citation of Related Structures:  
    1I94, 1I95, 1I96, 1I97

  • 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 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.


  • Organizational Affiliation

    Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, 14195 Berlin, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2255Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3238Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4208Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5161Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6101Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7155Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8138Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9128Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10104Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11128Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12131Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13125Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1460Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1588Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1688Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SJH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17104Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1887Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1992Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20105Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THX26Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RRNA1,514Thermus thermophilus
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WO2
Query on WO2

Download Ideal Coordinates CCD File 
AD [auth G]
BD [auth H]
CD [auth J]
ED [auth K]
GC [auth A]
AD [auth G],
BD [auth H],
CD [auth J],
ED [auth K],
GC [auth A],
HC [auth A],
IC [auth A],
JC [auth A],
KD [auth R],
PC [auth B],
QC [auth B],
RC [auth B],
VC [auth D],
YC [auth E]
OCTADECATUNGSTENYL DIPHOSPHATE
O62 P2 W18
WXCYUHHUPKCTBX-UHFFFAOYSA-A
TAC
Query on TAC

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KC [auth A]
LC [auth A]
MC [auth A]
NC [auth A]
OC [auth A]
KC [auth A],
LC [auth A],
MC [auth A],
NC [auth A],
OC [auth A],
WC [auth D]
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
GD [auth N],
UC [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
BA [auth A]
BB [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth K],
EA [auth A],
EB [auth A],
EC [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth L],
GA [auth A],
GB [auth A],
HA [auth A],
HB [auth A],
HD [auth P],
IA [auth A],
IB [auth A],
ID [auth Q],
JA [auth A],
JB [auth A],
JD [auth Q],
KA [auth A],
KB [auth A],
LA [auth A],
LB [auth A],
LD [auth T],
MA [auth A],
MB [auth A],
MD [auth T],
NA [auth A],
NB [auth A],
ND [auth T],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
SC [auth D],
TA [auth A],
TB [auth A],
TC [auth D],
UA [auth A],
UB [auth A],
V [auth A],
VA [auth A],
VB [auth A],
W [auth A],
WA [auth A],
WB [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth E],
Y [auth A],
YA [auth A],
YB [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 406.9α = 90
b = 406.9β = 90
c = 175.2γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations