9LUD | pdb_00009lud

Crystal structure of 9-mer peptide from H5N1 avian influenza virus in complex with B4 DUCK MHC I (UAA*76)

• PDB DOI: https://doi.org/10.2210/pdb9LUD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Anas platyrhynchos, H5N1 subtype
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-08 Released: 2026-02-11 
• Deposition Author(s): Gao, F., Li, Y.L., Dai, M.M., Liao, M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.247 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.183 (DCC) 

Starting Model: experimental

Literature

Efficient Identification of Tembusu Virus CTL Epitopes in Inbred HBW/B4 Ducks Using a Novel MHC Class I-Restricted Epitope Screening Scheme

Lin, Z., Zhang, N.Z.

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.14 kDa 
• Atom Count: 3,223 
• Modeled Residue Count: 379 
• Deposited Residue Count: 381 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	271	Anas platyrhynchos	Mutation(s): 0  Gene Names: Anpl-UAA01
UniProt
Find proteins for A0A6M3RI17 (Anas platyrhynchos) Explore A0A6M3RI17  Go to UniProtKB:  A0A6M3RI17

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	101	Anas platyrhynchos	Mutation(s): 0  Gene Names: b2m
UniProt
Find proteins for Q14U75 (Anas platyrhynchos) Explore Q14U75  Go to UniProtKB:  Q14U75

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-ARG-ASN-LEU-HIS-ILE-PRO-GLU-VAL	C	9	H5N1 subtype	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.247 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.183 (DCC) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.094	α = 90
b = 82.094	β = 90
c = 111.37	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-11 
Deposition Author(s): Gao, F., Li, Y.L., Dai, M.M., Liao, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-02-11
  Type: Initial release