4FQX

Crystal structure of HLA-DM bound to HLA-DR1

• PDB DOI: https://doi.org/10.2210/pdb4FQX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2012-06-25 Released: 2013-01-09 
• Deposition Author(s): Sethi, D.K., Pos, W., Wucherpfennig, K.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B2C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.7 kDa 
• Atom Count: 6,196 
• Modelled Residue Count: 751 
• Deposited Residue Count: 812 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DM alpha chain	A [auth C]	203	Homo sapiens	Mutation(s): 3  Gene Names: DM alpha chain, DMA, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, HLA-DMA, RING6
UniProt & NIH Common Fund Data Resources
Find proteins for P28067 (Homo sapiens) Explore P28067  Go to UniProtKB:  P28067
PHAROS:  P28067 GTEx:  ENSG00000204257

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DM beta chain	B [auth D]	199	Homo sapiens	Mutation(s): 2  Gene Names: DM beta chain, DMB, HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, HLA-DMB, RING7
UniProt & NIH Common Fund Data Resources
Find proteins for P28068 (Homo sapiens) Explore P28068  Go to UniProtKB:  P28068
PHAROS:  P28068 GTEx:  ENSG00000242574

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide	C [auth E]	11	N/A	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	D [auth A]	191	Homo sapiens	Mutation(s): 1  Gene Names: HLA-DR1 alpha chain, HLA-DRA, HLA-DRA1, MHC CLASS II MOLECULE
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-1 beta chain	E [auth B]	208	Homo sapiens	Mutation(s): 1  Gene Names: beta chain, HLA-DR1, HLA-DRB1, MHC CLASS II MOLECULE
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.240 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.19	α = 90
b = 121.649	β = 90
c = 138.416	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Sethi, D.K., Pos, W., Wucherpfennig, K.W.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary