6KYU | pdb_00006kyu

Complex assembly, crystallization and preliminary X-ray crystallographic studies of duck MHC class I molecule

• PDB DOI: https://doi.org/10.2210/pdb6KYU/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Anas platyrhynchos, Duck Tembusu virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-20 Released: 2020-09-23 
• Deposition Author(s): Liu, Z.X., Zhang, L., Zhang, N.Z.
• Funding Organization(s): National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 

Literature

Complex assembly, crystallization and preliminary X-ray crystallographic analysis of the duck pAnpl-UAA

Liu, Z.X., 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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.18 kDa 
• Atom Count: 3,671 
• 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: Apnl-UAA*B4
UniProt
Find proteins for A0A2Z4U0R6 (Anas platyrhynchos) Explore A0A2Z4U0R6  Go to UniProtKB:  A0A2Z4U0R6

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 U3I3I3 (Anas platyrhynchos platyrhynchos) Explore U3I3I3  Go to UniProtKB:  U3I3I3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide	C	9	Duck Tembusu virus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.468	α = 90
b = 82.468	β = 90
c = 112.507	γ = 120

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Liu, Z.X., Zhang, L., Zhang, N.Z.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2016YFD0500106

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2020-12-30
  Changes: Source and taxonomy
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary