8GM8 | pdb_00008gm8

Crystal structure of shark nonclassical MHC CLASS I, UFA

• PDB DOI: https://doi.org/10.2210/pdb8GM8/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Ginglymostoma cirratum
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-03-24 Released: 2024-11-27 
• Deposition Author(s): Castro, C.D., Adams, E.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Model: in silico

Literature

Characterization of Shark CD1 Establishes Its Presence in the Primordial MHC

Castro, C.D., Adams, E.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, homology

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration, homology

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, homology

Macromolecule Content 

• Total Structure Weight: 123.95 kDa 
• Atom Count: 7,672 
• Modeled Residue Count: 956 
• Deposited Residue Count: 1,080 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I protein	A, C, E	265	Ginglymostoma cirratum	Mutation(s): 0  Gene Names: Gici-UFA, UFA

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D, F	95	Ginglymostoma cirratum	Mutation(s): 0  Gene Names: B2M
UniProt
Find proteins for F4ZE04 (Ginglymostoma cirratum) Explore F4ZE04  Go to UniProtKB:  F4ZE04
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth B], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.274 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.065	α = 63.57
b = 89.865	β = 78.25
c = 90.08	γ = 80.35

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Castro, C.D., Adams, E.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI170844-01

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release