7M8S | pdb_00007m8s

Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395)

PDB DOI: https://doi.org/10.2210/pdb7M8S/pdb

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

Deposited: 2021-03-30 Released: 2021-06-23
Deposition Author(s): Gras, S., Nguyen, A.T., Szeto, C.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.247 (Depositor), 0.232 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules

Nguyen, A.T., Szeto, C., Jayasinghe, D., Lobos, C.A., Halim, H., Chatzileontiadou, D.S.M., Grant, E.J., Gras, S.

(2021) Biophysica 1

DOI: https://doi.org/10.3390/biophysica1020015

Macromolecule Content

Total Structure Weight: 90.09 kDa
Atom Count: 6,640
Modeled Residue Count: 769
Deposited Residue Count: 772
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A, D	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens) Explore A0A140T913 Go to UniProtKB: A0A140T913
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A140T913
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	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
Spike protein S1 peptide	C, F	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.247 (Depositor), 0.232 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.601	α = 90
b = 86.686	β = 90
c = 163.207	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
Aimless	data scaling
Coot	model building
XDS	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-23

Deposition Author(s):

Gras, S.

Nguyen, A.T.

Szeto, C.

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	1159272

Revision History (Full details and data files)

Version 1.0: 2021-06-23
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary