1YVP | pdb_00001yvp

Ro autoantigen complexed with RNAs

• PDB DOI: https://doi.org/10.2210/pdb1YVP/pdb
• NAKB: 1YVP

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Xenopus laevis
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2005-02-16 Released: 2005-06-07 
• Deposition Author(s): Stein, A.J., Fuchs, G., Fu, C., Wolin, S.L., Reinisch, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.238 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

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

• PubMed: 15907467 
• DOI: https://doi.org/10.1016/j.cell.2005.03.009
• Primary Citation Related Structures: 
  1YVP, 1YVR


• 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 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.

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Organizational Affiliation: 
• Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510.
Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510; Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06510.
Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06510. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 142.02 kDa 
• Atom Count: 9,890 
• Modeled Residue Count: 1,113 
• Deposited Residue Count: 1,136 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
60-kDa SS-A/Ro ribonucleoprotein	G [auth A], H [auth B]	538	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P42700 (Xenopus laevis) Explore P42700  Go to UniProtKB:  P42700

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Y RNA sequence, first strand	A [auth C], C [auth E], E [auth G], F [auth H]	10	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Y RNA sequence, second strand	B [auth D], D [auth F]	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	I [auth A], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	J [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.238 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.3	α = 90
b = 153.65	β = 92.8
c = 80.56	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
SOLVE	phasing
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Stein, A.J., Fuchs, G., Fu, C., Wolin, S.L., Reinisch, K.M.

Revision History  

• Version 1.0: 2005-06-07
  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: 2011-12-28
  Changes: Advisory
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations