9K2R | pdb_00009k2r

Human T cell receptor (TRAV2401/TRBV2701) in complex with HLA-C*1202 and IY11 peptide

PDB DOI: https://doi.org/10.2210/pdb9K2R/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-18 Released: 2025-09-17
Deposition Author(s): Chikata, T., Kuroki, K., Kuse, N., Kliszczak, A., Paes, W., Tomioka, N., Parker, R., Aflalo, A., Akahoshi, T., Yamashita, R., Sakata, R., Kusaka, H., Watanabe, Y., Nicastri, A., Matsubara, H., Ose, T., Kita, S., Oka, S., Gatanaga, H., Lin, Z., Ternette, N., Borrow, P., Maenaka, K., Takiguchi, M.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Human T cell receptor (TRAV2401/TRBV2701) in complex with HLA-C*1202 and IY11 peptide

Chikata, T., Kuroki, K., Kuse, N., Kliszczak, A., Paes, W., Tomioka, N., Parker, R., Aflalo, A., Akahoshi, T., Yamashita, R., Sakata, R., Kusaka, H., Watanabe, Y., Nicastri, A., Matsubara, H., Ose, T., Kita, S., Oka, S., Gatanaga, H., Lin, Z., Ternette, N., Borrow, P., Maenaka, K., Takiguchi, M.

To be published.

Macromolecule Content

Total Structure Weight: 286.43 kDa
Atom Count: 19,680
Modeled Residue Count: 2,426
Deposited Residue Count: 2,493
Unique protein chains: 5

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D, G	275	Homo sapiens	Mutation(s): 0 Gene Names: HLA-C
UniProt
Find proteins for A0A165EYK7 (Homo sapiens) Explore A0A165EYK7 Go to UniProtKB: A0A165EYK7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A165EYK7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E, H	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
peptide from p51 RT	C, F, I	11	Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)	Mutation(s): 0
UniProt
Find proteins for P12499 (Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)) Explore P12499 Go to UniProtKB: P12499
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12499
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	J, L, N	204	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain	K, M, O	241	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.207 (Depositor), 0.207 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 207.827	α = 90
b = 344.872	β = 90
c = 134.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	17fk0410302h0003
Japan Agency for Medical Research and Development (AMED)	Japan	21fk0410032h0003
Japan Society for the Promotion of Science (JSPS)	Japan	20H03726