3CUP | pdb_00003cup

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235

• PDB DOI: https://doi.org/10.2210/pdb3CUP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2008-04-16 Released: 2009-04-21 
• Deposition Author(s): Corper, A.L., Yoshida, K., Teyton, L., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 
  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235

Yoshida, K., Corper, A.L., Puckett, C., Sim, J., Valerie, M.-D., Jabri, B., Wilson, I.A., Teyton, L.

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: 47.62 kDa 
• Atom Count: 2,953 
• Modeled Residue Count: 358 
• Deposited Residue Count: 412 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-D alpha chain	A	190	Mus musculus	Mutation(s): 0  Gene Names: H2-Aa
UniProt
Find proteins for P04228 (Mus musculus) Explore P04228  Go to UniProtKB:  P04228
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II H2-IA-beta chain linked to GAD221-235 peptide	B	222	Mus musculus	Mutation(s): 0  EC: 4.1.1.15
UniProt
Find proteins for Q05683 (Rattus norvegicus) Explore Q05683  Go to UniProtKB:  Q05683
Find proteins for Q31135 (Mus musculus) Explore Q31135  Go to UniProtKB:  Q31135
UniProt Groups	Q31135Q05683

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free:  0.286 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.832	α = 90
b = 55.832	β = 90
c = 338.834	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Corper, A.L., Yoshida, K., Teyton, L., Wilson, I.A.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2017-06-28
  Changes: Advisory, Atomic model, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.2: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.3: 2024-10-09
  Changes: Structure summary