8JHW | pdb_00008jhw

The first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum

• PDB DOI: https://doi.org/10.2210/pdb8JHW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Cryptosporidium parvum
• Expression System: Escherichia coli, Synthecium
• Mutation(s): No 


• Deposited: 2023-05-25 Released: 2024-05-29 
• Deposition Author(s): Fan, S., Wang, Y.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free: 
  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

The first crystal structure of a H-2Kb-restricted decapeptide from Cryptosporidium parvum

Fan, S., Wang, Y.

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: 45.01 kDa 
• Atom Count: 3,159 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A	275	Mus musculus	Mutation(s): 0  Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Mus musculus	Mutation(s): 0  Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-THR-PHE-GLU-LYS-SER-TYR-ASN-THR-VAL	C	10	Cryptosporidium parvum	Mutation(s): 0
UniProt
Find proteins for A0A7S7LF56 (Cryptosporidium parvum) Explore A0A7S7LF56  Go to UniProtKB:  A0A7S7LF56

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.12 Å
• R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.240 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.94	α = 90
b = 86.94	β = 90
c = 293.73	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Fan, S., Wang, Y.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31702232

Revision History  

• Version 1.0: 2024-05-29
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary