8HT3

Crystal structure of immunoglobulin new antigen receptor variable domain from Okamejei kenojei

• PDB DOI: https://doi.org/10.2210/pdb8HT3/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Okamejei kenojei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-12-20 Released: 2023-07-05 
• Deposition Author(s): Wen, J., Li, P., Bi, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Identification and characterization of IgNAR and VNAR repertoire from the ocellate spot skate (Okamejei kenojei)

Wen, J., Gong, J., Li, P., Deng, P., Sun, M., Wu, Y., Tian, C., Wang, H., Bi, Y.

(2023) Front Mar Sci 10: 1183744

• DOI: https://doi.org/10.3389/fmars.2023.1183744

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.53 kDa 
• Atom Count: 863 
• Modelled Residue Count: 104 
• Deposited Residue Count: 104 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
New Antigen Receptor variable domain	A	104	Okamejei kenojei	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.901	α = 90
b = 72.213	β = 90
c = 70.139	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
XDS	data scaling
MrBUMP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-05 
Deposition Author(s): Wen, J., Li, P., Bi, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	41876168

Revision History  

• Version 1.0: 2023-07-05
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references
• Version 1.2: 2024-10-30
  Changes: Database references, Structure summary