9K2U | pdb_00009k2u

Crystal structure of HLA-C*1202 in complex with IY11V9A peptide

• PDB DOI: https://doi.org/10.2210/pdb9K2U/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HLA-C*1202 in complex with IY11V9A 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.07 kDa 
• Atom Count: 3,337 
• Modeled Residue Count: 380 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-C
UniProt
Find proteins for A0A165EYK7 (Homo sapiens) Explore A0A165EYK7  Go to UniProtKB:  A0A165EYK7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from p51 RT	C	11	Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)	Mutation(s): 0
UniProt
Find proteins for O89290 (Human immunodeficiency virus type 1 group M subtype F1 (isolate 93BR020)) Explore O89290  Go to UniProtKB:  O89290

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.138	α = 90
b = 100.555	β = 90
c = 113.744	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 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.

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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

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release