1JZV

Crystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA

Structural Biology Knowledgebase: 1JZV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.203

Literature

Macromolecules
Sequence Display for 1JZV

Classification: RNA

Total Structure Weight: 11258.68

Macromolecule Entities
Molecule Chains Length Organism Details
5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3' A, C 8 synthetic SL2 STEM-LOOP OF THE HIV-1 PSI-RNA
5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3' B, D 9 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MG
Query on MG

C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
5BU
Query on 5BU
A, C RNA LINKING C9 H12 Br N2 O9 P U
5IC
Query on 5IC
B, D RNA LINKING C9 H13 I N3 O8 P C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.203
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.80 α = 90.00
b = 45.80 β = 90.00
c = 89.65 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2001-09-17
  • Released Date: 2003-11-11
  • Deposition author(s): Xiong, Y., Sudarsanakumar, C., Deng, J., Pan, B., Sundaralingam, M.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4