4GXY

RNA structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch.

Peselis, A.Serganov, A.

(2012) Nat.Struct.Mol.Biol. 19: 1182-1184

  • DOI: 10.1038/nsmb.2405

  • PubMed Abstract: 
  • Coenzyme B(12) has a key role in various enzymatic reactions and controls expression of bacterial genes through riboswitches. Here we report the crystal structure of the Symbiobacterium thermophilum B(12) riboswitch bound to its ligand adenosylcobala ...

    Coenzyme B(12) has a key role in various enzymatic reactions and controls expression of bacterial genes through riboswitches. Here we report the crystal structure of the Symbiobacterium thermophilum B(12) riboswitch bound to its ligand adenosylcobalamin. The riboswitch forms a unique junctional structure with a large ligand-binding pocket tailored for specific recognition of the adenosyl moiety and flanked by structural elements that stabilize the regulatory region and enable control of gene expression.


    Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Adenosylcobalamin riboswitchA172N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B1Z
Query on B1Z

Download SDF File 
Download CCD File 
A
Adenosylcobalamin
Cobamamide
C72 H101 Co N18 O17 P
NAGDYSDXWHSJMC-OUCXYWSSSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
IRI
Query on IRI

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Download CCD File 
A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
A
RNA LINKINGC9 H13 N3 O10 P2C
GTP
Query on GTP
A
NON-POLYMERC10 H16 N5 O14 P3G
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.633α = 90.00
b = 96.633β = 90.00
c = 132.684γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXmodel building
MAR345data collection
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description