1XNR

Crystal Structure of an Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.235 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Structure of a purine-purine wobble base pair in the decoding center of the ribosome.

Murphy, F.V., Ramakrishnan, V.

(2004) Nat Struct Mol Biol 11: 1251-1252

  • DOI: https://doi.org/10.1038/nsmb866
  • Primary Citation of Related Structures:  
    1XNQ, 1XNR

  • PubMed Abstract: 

    Here we report the crystal structures of I.C and I.A wobble base pairs in the context of the ribosomal decoding center, clearly showing that the I.A base pair is of an I(anti).A(anti) conformation, as predicted by Crick. Additionally, the structures enable the observation of changes in the anticodon to allow purine-purine base pairing, the 'widest' base pair geometry allowed in the wobble position.

    • Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S2D [auth B]256Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S3E [auth C]239Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S4F [auth D]209Thermus thermophilusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S5G [auth E]162Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S6H [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S7I [auth G]156Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S8J [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S9K [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S10L [auth J]105Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S11M [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S12N [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S13O [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S14P [auth N]61Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S15Q [auth O]89Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S16R [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S17S [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S18T [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S19U [auth S]93Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein S20V [auth T]106Thermus thermophilusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
16S Ribosomal protein THXW [auth V]27Thermus 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
Anticodon tRNAB [auth X]11N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNAC [auth W]4N/A
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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 
X [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BE [auth D],
DE [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 X]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth X],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth J],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
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],
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 X],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.235 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.122α = 90
b = 401.122β = 90
c = 175.899γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
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: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Structure summary