8KCV | pdb_00008kcv

Crystal structure of UDA01-CAAMDDFQL

• PDB DOI: https://doi.org/10.2210/pdb8KCV/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: 2023-08-08 Released: 2024-08-14 
• 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: 2.39 Å
• R-Value Free: 
  0.251 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structure of duck MHC UDA01

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 88.66 kDa 
• Atom Count: 6,506 
• Modeled Residue Count: 762 
• Deposited Residue Count: 766 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	271	Anas platyrhynchos	Mutation(s): 0  Gene Names: Du6MHC I
UniProt
Find proteins for Q6I7L1 (Anas platyrhynchos) Explore Q6I7L1  Go to UniProtKB:  Q6I7L1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta2-microglobulin	B, E	103	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
peptide of AIV	C, F	9	unidentified influenza virus	Mutation(s): 0  EC: 3.1
UniProt
Find proteins for Q9Q0U9 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U9  Go to UniProtKB:  Q9Q0U9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.251 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.446	α = 90
b = 108.524	β = 90
c = 125.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-14 
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: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Structure summary