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- EMDB-41072: Human leukocyte antigen bound by two alloreactive antibody Fabs -

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Basic information

Entry
Database: EMDB / ID: EMD-41072
TitleHuman leukocyte antigen bound by two alloreactive antibody Fabs
Map data
Sample
  • Complex: L02/M07/A*01:01 complex
    • Protein or peptide: JTK191b_M07_Light
    • Protein or peptide: JTK191b_M07_Fab
    • Protein or peptide: JTK191b_L02_Light
    • Protein or peptide: JTK191b_L02_Fab
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: HLA_A0101_peptide
Keywordsantibody / human leukocyte antigen / graft rejection / IMMUNE SYSTEM
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / MHC class II protein complex / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / peptide antigen binding / positive regulation of T cell activation / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsKizziah JL / Killian JT / Diaz-Avalos R / Qiu S / Yang G / Green T / Lund FE
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)T32DK007545 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32AI007051 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI142737 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD024978 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA013148 United States
CitationJournal: Immunity / Year: 2025
Title: Topography of the HLA-A protein enforces shared and convergent immunodominant B cell and antibody alloresponses in transplant recipients.
Authors: John T Killian / R Glenn King / Aaron C K Lucander / James L Kizziah / Christopher F Fucile / Ruben Diaz-Avalos / Shihong Qiu / Aaron Silva-Sanchez / Betty J Mousseau / Kevin J Macon / ...Authors: John T Killian / R Glenn King / Aaron C K Lucander / James L Kizziah / Christopher F Fucile / Ruben Diaz-Avalos / Shihong Qiu / Aaron Silva-Sanchez / Betty J Mousseau / Kevin J Macon / Amanda R Callahan / Guang Yang / M Emon Hossain / Jobaida Akther / Daryl B Good / Susan Kelso / Julie A Houp / Frida Rosenblum / Paige M Porrett / Song C Ong / Vineeta Kumar / Erica Ollmann Saphire / John F Kearney / Troy D Randall / Alexander F Rosenberg / Todd J Green / Frances E Lund /
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 ...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-A01:01-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-A01:01. We demonstrated that the anti-HLA-A01:01 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-A01:01-mismatched transplant recipients. Thus, the B cell and antibody alloresponses appear tightly focused on a topographically defined region on the HLA-A01:01 crown that is conserved across individuals expressing distinct constellations of self-HLA-A.
History
DepositionJun 16, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41072.png

Downloads & links

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Map

FileDownload / File: emd_41072.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.6019725 - 0.984094
Average (Standard dev.)-0.00021797427 (±0.012459543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41072_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_41072_half_map_1.map
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Half map: #1

Fileemd_41072_half_map_2.map
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Sample components

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Entire : L02/M07/A*01:01 complex

EntireName: L02/M07/A*01:01 complex
Components
  • Complex: L02/M07/A*01:01 complex
    • Protein or peptide: JTK191b_M07_Light
    • Protein or peptide: JTK191b_M07_Fab
    • Protein or peptide: JTK191b_L02_Light
    • Protein or peptide: JTK191b_L02_Fab
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: HLA_A0101_peptide

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Supramolecule #1: L02/M07/A*01:01 complex

SupramoleculeName: L02/M07/A*01:01 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: JTK191b_M07_Light

MacromoleculeName: JTK191b_M07_Light / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.514057 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQDIN NYLNWYQQKP GKAPKLLVYD ASNLETGVPS RFSGSRSGTN FTFTISSLQP EDIATYSCQ HYVNLLFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQDIN NYLNWYQQKP GKAPKLLVYD ASNLETGVPS RFSGSRSGTN FTFTISSLQP EDIATYSCQ HYVNLLFTFG PGTKVDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #2: JTK191b_M07_Fab

MacromoleculeName: JTK191b_M07_Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.290279 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QITLKESGPT LVKPTQTLTL TCTFSGFSVN TSGVAVGWIR QPPGKALEWL ALIYWDHNKR YSPSLQNRLT ITKDTSQSQV VLTMTNVDP VDTATYYCGH TTGYCSGGSC YSGWFDPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QITLKESGPT LVKPTQTLTL TCTFSGFSVN TSGVAVGWIR QPPGKALEWL ALIYWDHNKR YSPSLQNRLT ITKDTSQSQV VLTMTNVDP VDTATYYCGH TTGYCSGGSC YSGWFDPWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK

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Macromolecule #3: JTK191b_L02_Light

MacromoleculeName: JTK191b_L02_Light / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.352977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLTQSPSF VSASVGDRIT ITCRASQGIK SYLAWYQQKP GKAPKLLIYV GSSLQSGVPS RFSGSGFGTE FTLTITSLQP EDFASYYCQ QLNDYPITFG GGTKVEITRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DVQLTQSPSF VSASVGDRIT ITCRASQGIK SYLAWYQQKP GKAPKLLIYV GSSLQSGVPS RFSGSGFGTE FTLTITSLQP EDFASYYCQ QLNDYPITFG GGTKVEITRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: JTK191b_L02_Fab

MacromoleculeName: JTK191b_L02_Fab / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.739482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCTVSRGSIE SYYWSWIRQP PGKGLEWIGY IHYTGSTKYN PSLGTRVSIS VDTSENQLSL NLKSVTPAD SAVYYCAKVD HYGSGVFWSF EFWGQGKSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLQESGPG LVKPSETLSL TCTVSRGSIE SYYWSWIRQP PGKGLEWIGY IHYTGSTKYN PSLGTRVSIS VDTSENQLSL NLKSVTPAD SAVYYCAKVD HYGSGVFWSF EFWGQGKSVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEP

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Macromolecule #5: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.992166 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQKMEPRAP WIEQEGPEYW DQETRNMKAH SQTDRANLGT LRGYYNQSE DGSHTIQIMY GCDVGPDGRF LRGYRQDAYD GKDYIALNED LRSWTAADMA AQITKRKWEA VHAAEQRRVY L EGRCVDGL RRYLENGKET LQR

UniProtKB: MHC class I antigen

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Macromolecule #6: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.879356 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MIQRTPKIQV YSRHPAENGK SNFLNCYVSG FHPSDIEVDL LKNGERIEKV EHSDLSFSKD WSFYLLYYTE FTPTEKDEYA CRVNHVTLS QPKIVKWDRD M

UniProtKB: Beta-2-microglobulin

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Macromolecule #7: HLA_A0101_peptide

MacromoleculeName: HLA_A0101_peptide / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.091191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VTEHDTLLY

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252746
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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