9Z51 | pdb_00009z51

HPV_Jin TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19)

PDB DOI: https://doi.org/10.2210/pdb9Z51/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Human papillomavirus 16
Expression System: Escherichia coli, Homo sapiens
Mutation(s): No

Deposited: 2025-11-11 Released: 2026-09-16
Deposition Author(s): Palowitch, G.M., Dulberger, C.L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.13 Å
R-Value Free:
0.267 (Depositor), 0.264 (DCC)
R-Value Work:
0.224 (Depositor), 0.225 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

HPV16 E7-specific NCI TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19)

Jackson, E.

To be published.

Macromolecule Content

Total Structure Weight: 393.17 kDa
Atom Count: 25,248
Modeled Residue Count: 3,245
Deposited Residue Count: 3,420
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A [auth C], F [auth G], K [auth L], P [auth S]	303	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens) Explore Q8WLS4 Go to UniProtKB: Q8WLS4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WLS4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B [auth D], G [auth H], L [auth M], Q [auth T]	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

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HPV_Jin TCR alpha chain (TRAV1-2*03)	C [auth A], H [auth E], M [auth J], R [auth Q]	200	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HPV_Jin TCR beta chain (TRBV5-6*01)	D [auth B], I [auth F], N [auth K], S [auth R]	243	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein E7	E [auth P], J [auth I], O [auth N], T [auth U]	9	Human papillomavirus 16	Mutation(s): 0
UniProt
Find proteins for P03129 (Human papillomavirus type 16) Explore P03129 Go to UniProtKB: P03129
Entity Groups
UniProt Group	P03129
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth J] SDF format, chain CA [auth K] SDF format, chain DA [auth Q] SDF format, chain EA [auth Q] SDF format, chain GA [auth R] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain X [auth E] SDF format, chain Z [auth F] MOL2 format, chain AA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth Q] MOL2 format, chain EA [auth Q] MOL2 format, chain GA [auth R] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth Q] mmCIF format, chain EA [auth Q] mmCIF format, chain GA [auth R] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth F]	AA [auth J] CA [auth K] DA [auth Q] EA [auth Q] GA [auth R] AA [auth J], CA [auth K], DA [auth Q], EA [auth Q], GA [auth R], U [auth A], W [auth B], X [auth E], Z [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth J] Focus chain CA [auth K] Focus chain DA [auth Q] Focus chain EA [auth Q] Focus chain GA [auth R] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth J] Focus chain CA [auth K] Focus chain DA [auth Q] Focus chain EA [auth Q] Focus chain GA [auth R] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth E] Focus chain Z [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth J] SDF format, chain FA [auth Q] SDF format, chain V [auth A] SDF format, chain Y [auth E] MOL2 format, chain BA [auth J] MOL2 format, chain FA [auth Q] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth E] mmCIF format, chain BA [auth J] mmCIF format, chain FA [auth Q] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth E]	BA [auth J], FA [auth Q], V [auth A], Y [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth J] Focus chain FA [auth Q] Focus chain V [auth A] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth J] Focus chain FA [auth Q] Focus chain V [auth A] Focus chain Y [auth E]