8T7R | pdb_00008t7r

Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens, Cytomegalovirus
  • Expression System: Homo sapiens, Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-06-21 Released: 2024-12-25 
  • Deposition Author(s): Green, T.J., Killian Jr, J.T., Qiu, S., Macon, K.J., Yang, G., King, R.G., Lund, F.E.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/Office of the Director, National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 
    0.263 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Topography of the HLA-A protein enforces shared and convergent immunodominant B cell and antibody alloresponses in transplant recipients.

Killian Jr., J.T.King, R.G.Lucander, A.C.K.Kizziah, J.L.Fucile, C.F.Diaz-Avalos, R.Qiu, S.Silva-Sanchez, A.Mousseau, B.J.Macon, K.J.Callahan, A.R.Yang, G.Hossain, M.E.Akther, J.Good, D.B.Kelso, S.Houp, J.A.Rosenblum, F.Porrett, P.M.Ong, S.C.Kumar, V.Saphire, E.O.Kearney, J.F.Randall, T.D.Rosenberg, A.F.Green, T.J.Lund, F.E.

(2025) Immunity 58: 3040-3060.e12

  • DOI: https://doi.org/10.1016/j.immuni.2025.10.014
  • Primary Citation of Related Structures:  
    8T6M, 8T7R

  • PubMed Abstract: 

    Donor-specific antibody responses against human leukocyte antigen (HLA) proteins mismatched between transplant donors and recipients cause allograft loss, yet the structural HLA epitopes targeted by alloreactive B cells and antibodies remain largely unresolved. We profiled the HLA-A 01:01-specific B cell response in the transplanted kidney and blood of a recipient undergoing antibody-mediated rejection and identified immunodominant B cell and antibody responses that emerged early in the alloimmune response. These responses were focused on topographically exposed mismatched HLA residues located in the α helices along the peptide-binding groove of HLA-A 01:01. We demonstrated that the anti-HLA-A 01:01 B cell alloresponse converged and was maintained on this same immunodominant HLA subregion, which comprises only 20% of the HLA molecule, in a diverse group of HLA-A 01:01-mismatched transplant recipients. Thus, the B cell and antibody alloresponses appear tightly focused on a topographically defined region on the HLA-A 01:01 crown that is conserved across individuals expressing distinct constellations of self-HLA-A.


  • Organizational Affiliation
    • Department of Surgery, The University of Alabama at Birmingham Heersink School of Medicine, Birmingham, AL 35294, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain from antibody JTK191b E07214Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chain from antibody JTK191b E07240Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen (Fragment)274Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for F6IQR9 (Homo sapiens)
Explore F6IQR9 
Go to UniProtKB:  F6IQR9
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UniProt GroupF6IQR9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
peptide9CytomegalovirusMutation(s): 0 
UniProt
Find proteins for P16790 (Human cytomegalovirus (strain AD169))
Explore P16790 
Go to UniProtKB:  P16790
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UniProt GroupP16790
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free:  0.263 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 357.076α = 90
b = 259.582β = 133.13
c = 255.361γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesT32AI007051
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI142737
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesT32DK007545
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA013148
National Institutes of Health/Office of the DirectorUnited StatesS10OD027000
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10RR025528
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10RR028976

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references