1XNQ

Structure of an Inosine-Adenine Wobble Base Pair Complex in the Context of the Decoding Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S2D [auth B]256Thermus thermophilusMutation(s): 0 
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Entity ID: 5
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Ribosomal protein S3E [auth C]239Thermus thermophilusMutation(s): 0 
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Entity ID: 6
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Ribosomal protein S4F [auth D]209Thermus thermophilusMutation(s): 0 
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Entity ID: 7
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Ribosomal protein S5G [auth E]162Thermus thermophilusMutation(s): 0 
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Entity ID: 8
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Ribosomal protein S6H [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 9
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Ribosomal protein S7I [auth G]156Thermus thermophilusMutation(s): 0 
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Entity ID: 10
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Ribosomal protein S8J [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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Ribosomal protein S9K [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 12
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Ribosomal protein S10L [auth J]105Thermus thermophilusMutation(s): 0 
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Ribosomal protein S11M [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 14
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Ribosomal protein S12N [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 15
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Ribosomal protein S13O [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 16
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Ribosomal protein S14P [auth N]61Thermus thermophilusMutation(s): 0 
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Entity ID: 17
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Ribosomal protein S15Q [auth O]89Thermus thermophilusMutation(s): 0 
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Entity ID: 18
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Ribosomal protein S16R [auth P]88Thermus thermophilusMutation(s): 0 
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Entity ID: 19
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Ribosomal protein S17S [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S18T [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein S19U [auth S]93Thermus thermophilusMutation(s): 0 
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Entity ID: 22
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Ribosomal protein S20V [auth T]106Thermus thermophilusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein THXW [auth V]27Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA1,522Thermus thermophilus
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Entity ID: 2
MoleculeChainsLengthOrganismImage
Anticodon tRNAB [auth X]11N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
mRNAC [auth W]4N/A
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Small Molecules
Ligands 3 Unique
IDChainsName / 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
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE [auth D],
CE [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth J],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.243 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.135α = 90
b = 401.135β = 90
c = 175.193γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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