1JK8 | pdb_00001jk8

Crystal structure of a human insulin peptide-HLA-DQ8 complex

PDB DOI: https://doi.org/10.2210/pdb1JK8/pdb

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

Deposited: 2001-07-11 Released: 2001-08-22
Deposition Author(s): Lee, K.H., Wucherpfennig, K.W., Wiley, D.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.258 (Depositor), 0.264 (DCC)
R-Value Work:
0.224 (Depositor), 0.232 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Models: experimental
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Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes.

Lee, K.H., Wucherpfennig, K.W., Wiley, D.C.

(2001) Nat Immunol 2: 501-507

PubMed: 11376336 Search on PubMed
DOI: https://doi.org/10.1038/88694
Primary Citation Related Structures:
1JK8

PubMed Abstract:
The class II major histocompatibility complex (MHC) glycoproteins HLA-DQ8 and HLA-DQ2 in humans and I-A(g7) in nonobese diabetic (NOD) mice are the major risk factors for increased susceptibility to type 1 diabetes. Using X-ray crystallography, we have determined the three-dimensional structure of DQ8 complexed with an immunodominant peptide from insulin. The similarity of the DQ8, DQ2 and I-A(g7) peptide-binding pockets suggests that diabetes is caused by the same antigen-presentation event(s) in humans and NOD mice. Correlating type 1 diabetes epidemiology and MHC sequences with the DQ8 structure suggests that other structural features of the P9 pocket in addition to position 57 contribute to susceptibility to type 1 diabetes.

Organizational Affiliation

Laboratory of Molecular Medicine, The Department of Medicine, The Children's Hospital, 320 Longwood Avenue, Boston, MA 02115, USA.

Macromolecule Content

Total Structure Weight: 44.72 kDa
Atom Count: 3,198
Modeled Residue Count: 385
Deposited Residue Count: 385
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ8	A	181	Homo sapiens	Mutation(s): 1 Gene Names: HLA-DQA1, DQA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01909 (Homo sapiens) Explore P01909 Go to UniProtKB: P01909
PHAROS: P01909 GTEx: ENSG00000196735
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01909
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P01909-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ8	B	190	Homo sapiens	Mutation(s): 0 Gene Names: HLA-DQB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01920 (Homo sapiens) Explore P01920 Go to UniProtKB: P01920
PHAROS: P01920
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01920
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
insulin B peptide	C	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308 Go to UniProtKB: P01308
PHAROS: P01308 GTEx: ENSG00000254647
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.258 (Depositor), 0.264 (DCC)
R-Value Work: 0.224 (Depositor), 0.232 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.034	α = 90
b = 42.862	β = 102.48
c = 87.467	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2001-08-22

Deposition Author(s):

Lee, K.H.

Wucherpfennig, K.W.

Wiley, D.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI39619

Revision History (Full details and data files)

Version 1.0: 2001-08-22
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: 2018-01-31
Changes: Advisory, Experimental preparation
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 2.0: 2024-09-18
Type: Coordinate replacement
Reason: Sequence discrepancy
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
Version 2.1: 2024-10-16
Changes: Structure summary