5Y91 | pdb_00005y91

The structure of the MHC class I molecule of bony fishes provides insights into the conserved nature of the antigen-presenting system

• PDB DOI: https://doi.org/10.2210/pdb5Y91/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Ctenopharyngodon idella, Sprivivirus cyprinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-22 Released: 2017-09-20 
• Deposition Author(s): Zhaosan, C., Nianzhi, Z., Chun, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of bony fish MHC class I complex at 1.9 Angstroms resolution.

Zhaosan, C., Nianzhi, Z., Chun, X.

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: 45.75 kDa 
• Atom Count: 3,401 
• Modeled Residue Count: 379 
• Deposited Residue Count: 400 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	275	Ctenopharyngodon idella	Mutation(s): 0  Gene Names: UAA106
UniProt
Find proteins for Q65XY8 (Ctenopharyngodon idella) Explore Q65XY8  Go to UniProtKB:  Q65XY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	116	Ctenopharyngodon idella	Mutation(s): 0  Gene Names: B2m
UniProt
Find proteins for Q65XZ7 (Ctenopharyngodon idella) Explore Q65XZ7  Go to UniProtKB:  Q65XZ7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE PHE-ALA-ASN-PHE-CYS-LEU-MET-MET-ILE	C	9	Sprivivirus cyprinus	Mutation(s): 0  EC: 3.6.1 (UniProt), 2.7.7.48 (UniProt), 2.7.7.88 (UniProt)
UniProt
Find proteins for Q91DR9 (Spring viremia of carp virus) Explore Q91DR9  Go to UniProtKB:  Q91DR9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.28	α = 90
b = 50.413	β = 124.08
c = 86.077	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Zhaosan, C., Nianzhi, Z., Chun, X.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary