9J4S | pdb_00009j4s

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

PDB DOI: https://doi.org/10.2210/pdb9J4S/pdb

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

Deposited: 2024-08-10 Released: 2025-08-13
Deposition Author(s): Yuan, P., Wu, D.C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.238 (Depositor), 0.238 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors

Yuan, P., Wu, D.C.

To be published.

Macromolecule Content

Total Structure Weight: 193.11 kDa
Atom Count: 13,301
Modeled Residue Count: 1,645
Deposited Residue Count: 1,676
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor CLA1 beta	A [auth G], C [auth A]	245	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor CLA1 alpha	B [auth I], D [auth B]	208	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B alpha chain	E [auth C], H [auth F]	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889 Go to UniProtKB: P01889
PHAROS: P01889 GTEx: ENSG00000234745
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01889
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	F [auth D], I [auth H]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	G [auth E], J	9	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9
Entity Groups
UniProt Group	P0DTC9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth A] SDF format, chain M [auth I] SDF format, chain L [auth I] SDF format, chain K [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth I] MOL2 format, chain L [auth I] MOL2 format, chain K [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth I] mmCIF format, chain L [auth I] mmCIF format, chain K [auth G]	K [auth G] L [auth I] M [auth I] N [auth A] O [auth C] K [auth G], L [auth I], M [auth I], N [auth A], O [auth C], P [auth D], Q [auth D], S [auth F], T [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth G] Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain K [auth G] Focus chain L [auth I] Focus chain M [auth I] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth F] Focus chain T [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]