8JQT | pdb_00008jqt

Crystal structure of U03-GPAKGIEYD

• PDB DOI: https://doi.org/10.2210/pdb8JQT/pdb

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


• Deposited: 2023-06-14 Released: 2024-06-19 
• 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: 1.99 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure of duck MHC U03

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: 44.68 kDa 
• Atom Count: 3,484 
• Modeled Residue Count: 380 
• Deposited Residue Count: 383 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen alpha chain	A	271	Anas platyrhynchos	Mutation(s): 0  Gene Names: Anpl-U, Anpl-UAA
UniProt
Find proteins for Q6JWQ7 (Anas platyrhynchos) Explore Q6JWQ7  Go to UniProtKB:  Q6JWQ7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	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	9	unidentified influenza virus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.282	α = 90
b = 126.282	β = 90
c = 65.167	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
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: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary