1YVP

Ro autoantigen complexed with RNAs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Insights into RNA Quality Control: The Ro Autoantigen Binds Misfolded RNAs via Its Central Cavity

Stein, A.J.Fuchs, G.Fu, C.Wolin, S.L.Reinisch, K.M.

(2005) Cell 121: 529-539

  • DOI: 10.1016/j.cell.2005.03.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ro 60 kDa autoantigen is a major target of the immune response in patients with systemic lupus erythematosus. In vertebrate cells, Ro binds misfolded small RNAs and likely functions in RNA quality control. In eukaryotes and bacteria, Ro also asso ...

    The Ro 60 kDa autoantigen is a major target of the immune response in patients with systemic lupus erythematosus. In vertebrate cells, Ro binds misfolded small RNAs and likely functions in RNA quality control. In eukaryotes and bacteria, Ro also associates with small RNAs called Y RNAs. We present structures of unliganded Ro and Ro complexed with two RNAs at 1.95 and 2.2 A resolution, respectively. Ro consists of a von Willebrand factor A domain and a doughnut-shaped domain composed of HEAT repeats. In the complex, a fragment of Y RNA binds on the outer surface of the HEAT-repeat ring, and single-stranded RNA binds in the toroid hole. Mutagenesis supports a binding site for misfolded RNAs that encompasses both sites, with a single-stranded end inserted into the toroid cavity. Our experiments suggest that one role of Y RNAs may be to regulate access of other RNAs to Ro.


    Organizational Affiliation

    Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60-kDa SS-A/Ro ribonucleoprotein
A, B
538Xenopus laevisMutation(s): 0 
Gene Names: trove2
Find proteins for P42700 (Xenopus laevis)
Go to UniProtKB:  P42700
Entity ID: 1
MoleculeChainsLengthOrganism
Y RNA sequence, first strandC,E,G,H10N/A
Entity ID: 2
MoleculeChainsLengthOrganism
Y RNA sequence, second strandD,F10N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
IU
Query on IU
C, D, E, F, G, H
RNA LINKINGC9 H12 I N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.300α = 90.00
b = 153.650β = 92.80
c = 80.560γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-12-28
    Type: Advisory