9YZ3 | pdb_00009yz3

Ro60 peptide bound to human HLA-DR3

PDB DOI: https://doi.org/10.2210/pdb9YZ3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-10-29 Released: 2026-09-09
Deposition Author(s): Lim, Z.F.S., Ting, Y.T., Ooi, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free:
0.272 (Depositor), 0.287 (DCC)
R-Value Work:
0.227 (Depositor), 0.240 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Ro60 peptide bound to human HLA-DR3

Lim, Z.F.S., Ting, Y.T., Ooi, J.

To be published.

Macromolecule Content

Total Structure Weight: 87.51 kDa
Atom Count: 6,126
Modeled Residue Count: 751
Deposited Residue Count: 752
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, C	177	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903 Go to UniProtKB: P01903
PHAROS: P01903 GTEx: ENSG00000204287
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01903
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen DR beta chain	B, D	186	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DRB1, RP1-93N13.1-001
UniProt
Find proteins for Q5Y7D1 (Homo sapiens) Explore Q5Y7D1 Go to UniProtKB: Q5Y7D1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5Y7D1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein RO60	E, F	13	Homo sapiens	Mutation(s): 0 Gene Names: RO60, SSA2, TROVE2
UniProt & NIH Common Fund Data Resources
Find proteins for P10155 (Homo sapiens) Explore P10155 Go to UniProtKB: P10155
PHAROS: P10155 GTEx: ENSG00000116747
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10155
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.87 Å
R-Value Free: 0.272 (Depositor), 0.287 (DCC)
R-Value Work: 0.227 (Depositor), 0.240 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.621	α = 90
b = 96.843	β = 98.6
c = 102.595	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
pointless	data scaling
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-09

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2026-09-09
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.