9D96 | pdb_00009d96

KIR3DL1 - HLA-B38-YHL complex

• PDB DOI: https://doi.org/10.2210/pdb9D96/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, human gammaherpesvirus 4
• Expression System: Escherichia coli, synthetic construct, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-21 Released: 2025-09-03 
• Deposition Author(s): Zhu, S., Vivian, J., Petersen, J., Rossjohn, J.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

The ancient MHC class I molecule HLA-B*38:01 calibrates the immune system to protect against multiple sclerosis

Ladell, K., Zhu, S., Kaufmann, M., Vivian, J., Petersen, J., Fugger, L., Rossjohn, J., Price, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Biological Assembly Evidence: gel filtration, surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.97 kDa 
• Atom Count: 5,500 
• Modeled Residue Count: 675 
• Deposited Residue Count: 687 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLA-DRB1
UniProt
Find proteins for E5FQ58 (Homo sapiens) Explore E5FQ58  Go to UniProtKB:  E5FQ58

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Epstein-Barr nuclear antigen 2	C	10	human gammaherpesvirus 4	Mutation(s): 0  Gene Names: EBNA2, BYRF1
UniProt
Find proteins for P12978 (Epstein-Barr virus (strain B95-8)) Explore P12978  Go to UniProtKB:  P12978

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell immunoglobulin-like receptor 3DL1	D [auth G]	301	Homo sapiens	Mutation(s): 0  Gene Names: KIR3DL1, CD158E, NKAT3, NKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P43629 (Homo sapiens) Explore P43629  Go to UniProtKB:  P43629
PHAROS:  P43629 GTEx:  ENSG00000167633
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P43629-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth G], F [auth G], G	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.346	α = 95.06
b = 60.588	β = 95.61
c = 63.288	γ = 106.37

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Zhu, S., Vivian, J., Petersen, J., Rossjohn, J.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release