6ZWA

CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype

• PDB DOI: https://doi.org/10.2210/pdb6ZWA/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Gallus gallus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-07-28 Released: 2021-08-11 
• Deposition Author(s): Halabi, S., Brear, P., Kaufman, J.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.252 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Literature

CLIP peptide bound to chicken MHC class II BL-2 from B19 haplotype

Halabi, S., Kaufman, 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)

Macromolecule Content

• Total Structure Weight: 45.76 kDa 
• Atom Count: 3,212 
• Modelled Residue Count: 376 
• Deposited Residue Count: 402 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II alpha chain	A	183	Gallus gallus	Mutation(s): 0  Gene Names: B-LA
UniProt
Find proteins for Q4U5Z6 (Gallus gallus) Explore Q4U5Z6  Go to UniProtKB:  Q4U5Z6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Invariant chain isoform p41,MHC class II beta chain 2	B	219	Gallus gallus	Mutation(s): 0  Gene Names: Ii, CD74, BLB2
UniProt
Find proteins for Q6J613 (Gallus gallus) Explore Q6J613  Go to UniProtKB:  Q6J613
Find proteins for A5HUL4 (Gallus gallus) Explore A5HUL4  Go to UniProtKB:  A5HUL4
UniProt Groups	Q6J613A5HUL4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.252 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.863	α = 90
b = 60.536	β = 107.88
c = 53.855	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Halabi, S., Brear, P., Kaufman, J.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	110106/Z/15/Z

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description