3TO2

Structure of HLA-A*0201 complexed with peptide Md3-C9 derived from a clustering region of restricted cytotoxic T lymphocyte epitope from SARS-CoV M protein

PDB DOI: https://doi.org/10.2210/pdb3TO2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, SARS coronavirus TJF
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-03 Released: 2012-08-29
Deposition Author(s): Liu, J., Qi, J., Gao, F., Yan, J., Gao, G.F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.230
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Functional and Structural Definition of a Clustering Region of HLA-A2-restricted Cytotoxic T Lymphocyte Epitopes

Liu, J., Qi, J., Gao, F., Yan, J., Gao, G.F.

(2011) Sci Technology Rev 29: 19-26

DOI: https://doi.org/10.3981/j.issn.1000-7857.2011.27.001

Macromolecule Content

Total Structure Weight: 44.64 kDa
Atom Count: 3,256
Modelled Residue Count: 384
Deposited Residue Count: 384
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	275	Homo sapiens	Mutation(s): 0 Gene Names: HLA
UniProt
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42 Go to UniProtKB: Q53Z42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q53Z42
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Md3-C9 peptide derived from Membrane glycoprotein	C	9	SARS coronavirus TJF	Mutation(s): 0
UniProt
Find proteins for P59596 (Severe acute respiratory syndrome coronavirus) Explore P59596 Go to UniProtKB: P59596
Entity Groups
UniProt Group	P59596
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.230
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.459	α = 90
b = 147.459	β = 90
c = 49.903	γ = 120

Software Package:

Software Name	Purpose
APEX	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Structure summary

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.