1UVQ

Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide

• PDB DOI:  https://doi.org/10.2210/pdb1UVQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2004-01-22 Released: 2004-02-05 
• Deposition Author(s): Siebold, C., Hansen, B.E., Wyer, J.R., Harlos, K., Esnouf, R.E., Svejgaard, A., Bell, J.I., Strominger, J.L., Jones, E.Y., Fugger, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Crystal Structure of Hla-Dq0602 that Protects Against Type 1 Diabetes and Confers Strong Susceptibility to Narcolepsy

Siebold, C., Hansen, B.E., Wyer, J.R., Harlos, K., Esnouf, R.E., Svejgaard, A., Bell, J.I., Strominger, J.L., Jones, E.Y., Fugger, L.

(2004) Proc Natl Acad Sci U S A 101: 1999

• PubMed: 14769912 
• DOI: https://doi.org/10.1073/pnas.0308458100
• Primary Citation of Related Structures:  
  1UVQ


• PubMed Abstract: 
  

The MHC class II molecule DQ0602 confers strong susceptibility to narcolepsy but dominant protection against type 1 diabetes. The crystal structure of DQ0602 reveals the molecular features underlying these contrasting genetic properties. Structural comparisons to homologous DQ molecules with differential disease associations highlight a previously unrecognized interplay between the volume of the P6 pocket and the specificity of the P9 pocket, which implies that presentation of an expanded peptide repertoire is critical for dominant protection against type 1 diabetes. In narcolepsy, the volume of the P4 pocket appears central to the susceptibility, suggesting that the presentation of a specific peptide population plays a major role.

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Organizational Affiliation: 

Division of Structural Biology, The Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 49.79 kDa 
• Atom Count: 3,532 
• Modelled Residue Count: 383 
• Deposited Residue Count: 428 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN	A	197	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQA1
UniProt
Find proteins for E9PMV2 (Homo sapiens) Explore E9PMV2  Go to UniProtKB:  E9PMV2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS II HISTOCOMPATIBILITY ANTIGEN	B	198	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1, HLA-DQB
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens) Explore P01920  Go to UniProtKB:  P01920
PHAROS:  P01920

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
OREXIN	C	33	Homo sapiens	Mutation(s): 0  Gene Names: HCRT, OX, PPORX, PPOX
UniProt & NIH Common Fund Data Resources
Find proteins for O43612 (Homo sapiens) Explore O43612  Go to UniProtKB:  O43612
PHAROS:  O43612

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLY	E [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	I [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.078	α = 90
b = 129.304	β = 90
c = 40.619	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-05 
Deposition Author(s): Siebold, C., Hansen, B.E., Wyer, J.R., Harlos, K., Esnouf, R.E., Svejgaard, A., Bell, J.I., Strominger, J.L., Jones, E.Y., Fugger, L.

Revision History  

• Version 1.0: 2004-02-05
  Type: Initial release
  
• Version 1.1: 2015-10-21
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary