6ID4

Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Defining the structural basis for human alloantibody binding to human leukocyte antigen allele HLA-A*11:01.

Gu, Y.Wong, Y.H.Liew, C.W.Chan, C.E.Z.Murali, T.M.Yap, J.Too, C.T.Purushotorman, K.Hamidinia, M.El Sahili, A.Goh, A.T.H.Teo, R.Z.C.Wood, K.J.Hanson, B.J.Gascoigne, N.R.J.Lescar, J.Vathsala, A.MacAry, P.A.

(2019) Nat Commun 10: 893-893

  • DOI: 10.1038/s41467-019-08790-1

  • PubMed Abstract: 
  • Our understanding of the conformational and electrostatic determinants that underlie targeting of human leukocyte antigens (HLA) by anti-HLA alloantibodies is principally based upon in silico modelling. Here we provide a biochemical/biophysical and f ...

    Our understanding of the conformational and electrostatic determinants that underlie targeting of human leukocyte antigens (HLA) by anti-HLA alloantibodies is principally based upon in silico modelling. Here we provide a biochemical/biophysical and functional characterization of a human monoclonal alloantibody specific for a common HLA type, HLA-A*11:01. We present a 2.4 Å resolution map of the binding interface of this antibody on HLA-A*11:01 and compare the structural determinants with those utilized by T-cell receptor (TCR), killer-cell immunoglobulin-like receptor (KIR) and CD8 on the same molecule. These data provide a mechanistic insight into the paratope-epitope relationship between an alloantibody and its target HLA molecule in a biological context where other immune receptors are concomitantly engaged. This has important implications for our interpretation of serologic binding patterns of anti-HLA antibodies in sensitized individuals and thus, for the biology of human alloresponses.


    Organizational Affiliation

    Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-11 alpha chain
A, E
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P13746 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P13746
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, F
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Heavy chain
C, H
283N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Light chain
D, L
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
peptide
T, U
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A, B, E, F
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.560α = 90.00
b = 215.330β = 92.96
c = 80.980γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
BUSTERrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-03-06
    Type: Data collection, Database references, Structure summary