5GJX | pdb_00005gjx

Crystal structure of DUCK MHC I for 2.06 angstrom

• PDB DOI: https://doi.org/10.2210/pdb5GJX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Anas platyrhynchos, unidentified influenza virus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-02 Released: 2017-05-10 
• Deposition Author(s): Wu, Y., Xia, C.
• Funding Organization(s): National Key Basic Research Program of China, National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structural Definition Of Duck MHC Class I For 2.06 Angstrom Explains its Resistance to Influenza A virus

Wu, Y., Xia, C.

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)

Macromolecule Content 

• Total Structure Weight: 44.61 kDa 
• Atom Count: 3,250 
• Modeled Residue Count: 379 
• Deposited Residue Count: 386 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	273	Anas platyrhynchos	Mutation(s): 1  Gene Names: Du5MHC I
UniProt
Find proteins for Q6I7L2 (Anas platyrhynchos) Explore Q6I7L2  Go to UniProtKB:  Q6I7L2

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 Q14U75 (Anas platyrhynchos) Explore Q14U75  Go to UniProtKB:  Q14U75

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-LEU-ILE-GLN-ASN-SER-ILE-THR-ILE	C	9	unidentified influenza virus	Mutation(s): 0
UniProt
Find proteins for Q9Q0U8 (Influenza A virus (strain A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd)) Explore Q9Q0U8  Go to UniProtKB:  Q9Q0U8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.487	α = 90
b = 63.538	β = 106.1
c = 79.954	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-10 
Deposition Author(s): Wu, Y., Xia, C.

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Funding Organization	Location	Grant Number
National Key Basic Research Program of China	China	2013CB835302
National Natural Science Foundation of China	China	No. 31572493

Revision History  

• Version 1.0: 2017-05-10
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary