9K2S | pdb_00009k2s

Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 peptide

PDB DOI: https://doi.org/10.2210/pdb9K2S/pdb

Classification: IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE), Homo sapiens
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: 2.40 Å
R-Value Free:
0.299 (Depositor), 0.299 (DCC)
R-Value Work:
0.245 (Depositor), 0.244 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Killer cell immunoglobulin-like receptor 2DL2 in complex with HLA-C*1202 and IY10 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: 69.05 kDa
Atom Count: 4,711
Modeled Residue Count: 564
Deposited Residue Count: 606
Unique protein chains: 4

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from p51 RT	A [auth D]	10	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	B [auth A]	276	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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C [auth B]	119	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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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
KIR2DL2	D [auth C]	201	Homo sapiens	Mutation(s): 0 Gene Names: KIR2DL2, KIR2DL3
UniProt
Find proteins for Q8N742 (Homo sapiens) Explore Q8N742 Go to UniProtKB: Q8N742
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N742
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.299 (Depositor), 0.299 (DCC)
R-Value Work: 0.245 (Depositor), 0.244 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.493	α = 90
b = 44.585	β = 111.45
c = 88.243	γ = 90

Software Package:

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

Structure Validation

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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	20H03726
Japan Society for the Promotion of Science (JSPS)	Japan	17fk0410302h0003
Japan Society for the Promotion of Science (JSPS)	Japan	21fk0410032h0003