8WO9 | pdb_00008wo9

Duck major histocompatibility complex class-1 02JD-IMFSNKMAR

• PDB DOI: https://doi.org/10.2210/pdb8WO9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Anas platyrhynchos, unidentified influenza virus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, synthetic construct
• Mutation(s): No 


• Deposited: 2023-10-06 Released: 2024-10-09 
• Deposition Author(s): Tang, Z., Zhang, N.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structure of duck MHC 02JD

Tang, Z., Zhang, N.

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: 44.58 kDa 
• Atom Count: 3,630 
• Modeled Residue Count: 380 
• Deposited Residue Count: 384 
• 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	104	Anas platyrhynchos	Mutation(s): 0  Gene Names: b2m
UniProt
Find proteins for U3I3I3 (Anas platyrhynchos platyrhynchos) Explore U3I3I3  Go to UniProtKB:  U3I3I3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide of AIV	C	9	unidentified influenza virus	Mutation(s): 0  EC: 2.7.7.48
UniProt
Find proteins for Q9Q0V0 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0V0  Go to UniProtKB:  Q9Q0V0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.92	α = 90
b = 46.3	β = 102.81
c = 95.47	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Tang, Z., Zhang, N.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32172871

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release