7UR1 | pdb_00007ur1

SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01

PDB DOI: https://doi.org/10.2210/pdb7UR1/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2022-04-21 Released: 2023-04-26
Deposition Author(s): Szeto, C., Ahn, Y.M., Gras, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.277 (Depositor), 0.276 (DCC)
R-Value Work:
0.234 (Depositor), 0.235 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01

Szeto, C., Ahn, Y.M., Gras, S.

To be published.

Macromolecule Content

Total Structure Weight: 54.01 kDa
Atom Count: 3,188
Modeled Residue Count: 386
Deposited Residue Count: 475
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I antigen	A	365	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A, HLA
UniProt
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42 Go to UniProtKB: Q53Z42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53Z42
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, CDABP0092, HDCMA22P
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
SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL)	C	10	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.277 (Depositor), 0.276 (DCC)
R-Value Work: 0.234 (Depositor), 0.235 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.651	α = 90
b = 81.696	β = 90
c = 110.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	Australia	--

Revision History (Full details and data files)

Version 1.0: 2023-04-26
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: 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.