1K8I

CRYSTAL STRUCTURE OF MOUSE H2-DM

• PDB DOI: https://doi.org/10.2210/pdb1K8I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2001-10-24 Released: 2001-12-05 
• Deposition Author(s): Fremont, D.H., Crawford, F., Marrack, P., Hendrickson, W., Kappler, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Crystal structure of mouse H2-M.

Fremont, D.H., Crawford, F., Marrack, P., Hendrickson, W.A., Kappler, J.

(1998) Immunity 9: 385-393

• PubMed: 9768758 
• DOI: https://doi.org/10.1016/s1074-7613(00)80621-4
• Primary Citation of Related Structures:  
  1K8I


• PubMed Abstract: 
  

  H2-M (HLA-DM in humans) resides in an acidic endosomal compartment, where it facilitates the loading of antigenic peptides into the peptide-binding groove of class II MHC. The crystal structure of a soluble form of H2-M has been solved to 3.1 A resolution, revealing a heterodimer with structural similarities to the MHC family of proteins. In contrast to its antigen-presenting cousins, the membrane distal alpha helices of H2-M pack closely together, occluding most of the binding groove except for a single large pocket near the center. The structure of H2-M has several unique features that may play a role in its function as a molecular chaperone and peptide exchange factor.

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Organizational Affiliation: 

Center for Immunology, Department of Pathology, Washington University School of Medicine, St. Louis, Missouri 63110, USA. [e-mail]

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: 43.24 kDa 
• Atom Count: 2,962 
• Modelled Residue Count: 371 
• Deposited Residue Count: 382 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II H2-M alpha chain	A	191	Mus musculus	Mutation(s): 0  Gene Names: H2-DM
UniProt
Find proteins for P28078 (Mus musculus) Explore P28078  Go to UniProtKB:  P28078
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P28078-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II H2-M beta 2 chain	B	191	Mus musculus	Mutation(s): 0  Gene Names: H2-DM
UniProt
Find proteins for Q31099 (Mus musculus) Explore Q31099  Go to UniProtKB:  Q31099

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [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: 3.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.7	α = 90
b = 142.7	β = 90
c = 76.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-12-05 
Deposition Author(s): Fremont, D.H., Crawford, F., Marrack, P., Hendrickson, W., Kappler, J.

Revision History  

• Version 1.0: 2001-12-05
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary