3TO2 | pdb_00003to2

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 (Depositor), 0.240 (DCC)
R-Value Work:
0.193 (Depositor), 0.205 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3TO2

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
Modeled Residue Count: 384
Deposited Residue Count: 384
Unique protein chains: 3

Macromolecules

Find similar proteins by:

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 & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04439
Sequence Annotations Expand
Reference Sequence

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.240 (DCC)
R-Value Work: 0.193 (Depositor), 0.205 (DCC)
R-Value Observed: 0.195 (Depositor)

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

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View more in-depth experimental data

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

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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.