1IBK

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 

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This is version 1.3 of the entry. See complete history. 


Literature

Recognition of cognate transfer RNA by the 30S ribosomal subunit.

Ogle, J.M., Brodersen, D.E., Clemons Jr., W.M., Tarry, M.J., Carter, A.P., Ramakrishnan, V.

(2001) Science 292: 897-902

  • DOI: https://doi.org/10.1126/science.1060612
  • Primary Citation of Related Structures:  
    1IBK, 1IBL, 1IBM

  • PubMed Abstract: 

    Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3D [auth C]239Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4E [auth D]209Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5F [auth E]162Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6G [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7H [auth G]156Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8I [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9J [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10K [auth J]105Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11L [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12M [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13N [auth M]126Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14O [auth N]61Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15P [auth O]89Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16Q [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17R [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18S [auth R]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19T [auth S]93Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20U [auth T]106Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THX26Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA1,522Thermus thermophilus
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Entity ID: 2
MoleculeChains LengthOrganismImage
P-SITE MESSENGER RNA FRAGMENTB [auth X]6Thermus thermophilus
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR
Download Ideal Coordinates CCD File 
W [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
FE [auth D],
HE [auth N]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth D],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth L],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.16α = 90
b = 401.16β = 90
c = 176.36γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-04
    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: 2022-12-21
    Changes: Database references, Derived calculations, Structure summary