6ATF

HLA-DRB1*1402 in complex with Vimentin59-71

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report



Literature

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.

Scally, S.W., Law, S.C., Ting, Y.T., Heemst, J.V., Sokolove, J., Deutsch, A.J., Bridie Clemens, E., Moustakas, A.K., Papadopoulos, G.K., Woude, D.V., Smolik, I., Hitchon, C.A., Robinson, D.B., Ferucci, E.D., Bernstein, C.N., Meng, X., Anaparti, V., Huizinga, T., Kedzierska, K., Reid, H.H., Raychaudhuri, S., Toes, R.E., Rossjohn, J., El-Gabalawy, H., Thomas, R.

(2017) Ann Rheum Dis 76: 1915-1923

  • DOI: 10.1136/annrheumdis-2017-211300
  • Primary Citation of Related Structures:  
    6ATF, 6ATZ, 6ATI

  • PubMed Abstract: 

    • The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a c ...

    The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the 'shared susceptibility epitope (SE)'. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection. Indigenous North American (INA) populations have high risk of early-onset ACPA-positive RA, whereby HLA-DRB1*04:04 and HLA-DRB1*14:02 are implicated as risk factors for RA in INA. However, HLA-DRB1*14:02 has a His13βSer polymorphism. Therefore, we aimed to verify this association and determine its molecular mechanism.

    Organizational Affiliation: 

    The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HLA class II histocompatibility antigen, DR alpha chainA, D189Homo sapiensMutation(s): 0 
Gene Names: HLA-DRA, HLA-DRA1
Find proteins for P01903 (Homo sapiens)
Explore P01903 
Go to UniProtKB:  P01903
NIH Common Fund Data Resources
PHAROS  P01903
GTEx  ENSG00000204287
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MHC class II antigenB, E200Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for A0A0A1I7H6 (Homo sapiens)
Explore A0A0A1I7H6 
Go to UniProtKB:  A0A0A1I7H6
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vimentin59-71C, F13synthetic constructMutation(s): 0 
Find proteins for P08670 (Homo sapiens)
Explore P08670 
Go to UniProtKB:  P08670
NIH Common Fund Data Resources
PHAROS  P08670
GTEx  ENSG00000026025
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
2 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
PGE
Query on PGE
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
B, E
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.98α = 90
b = 77.77β = 109.52
c = 94.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
NHMRC, ARCAustralia--

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary