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- EMDB-73460: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1 -

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Basic information

Entry
Database: EMDB / ID: EMD-73460
TitleTCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
Map data
Sample
  • Complex: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Melanoma-associated antigen 3
    • Protein or peptide: AD01-VHH
    • Protein or peptide: vAB30 light chain
    • Protein or peptide: vAB30 heavy chain
KeywordsHLA / TCR mimic antibody / de novo design / immune complex / IMMUNE SYSTEM
Function / homology
Function and homology information


caspase binding / negative regulation of protein processing / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of autophagy / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport ...caspase binding / negative regulation of protein processing / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of autophagy / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / 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 / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / histone deacetylase binding / 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 / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / 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 / Melanoma-associated antigen 3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang N / Jude KM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Cancer Research UKCGCATF-2023/100006 United Kingdom
CitationJournal: bioRxiv / Year: 2025
Title: Targeting peptide-MHC complexes with designed T cell receptors and antibodies.
Authors: Amir Motmaen / Kevin M Jude / Nan Wang / Anastasia Minervina / David Feldman / Mauriz A Lichtenstein / Abishai Ebenezer / Colin Correnti / Paul G Thomas / K Christopher Garcia / David Baker / Philip Bradley
Abstract: Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise ...Class I major histocompatibility complexes (MHCs), expressed on the surface of all nucleated cells, present peptides derived from intracellular proteins for surveillance by T cells. The precise recognition of foreign or mutated peptide-MHC (pMHC) complexes by T cell receptors (TCRs) is central to immune defense against pathogens and tumors. Although patient-derived TCRs specific for cancer-associated antigens have been used to engineer tumor-targeting therapies, their reactivity toward self- or near-self antigens may be constrained by negative selection in the thymus. Here, we introduce a structure-based deep learning framework, ADAPT (Antigen-receptor Design Against Peptide-MHC Targets), for the design of TCRs and antibodies that bind to pMHC targets of interest. We evaluate the ADAPT pipeline by designing and characterizing TCRs and antibodies against a diverse panel of pMHCs. Cryogenic electron microscopy structures of two designed antibodies bound to their respective pMHC targets demonstrate atomic-level accuracy at the recognition interface, supporting the robustness of our structure-based approach. Computationally designed TCRs and antibodies targeting pMHC complexes could enable a broad range of therapeutic applications, from cancer immunotherapy to autoimmune disease treatment, and insights gained from TCR-pMHC design should advance predictive understanding of TCR specificity with implications for basic immunology and clinical diagnostics.
History
DepositionOct 20, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73460.png

Downloads & links

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Map

FileDownload / File: emd_73460.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264.648 Å		1.1 Å/pix.
x 240 pix.
= 264.648 Å		1.1 Å/pix.
x 240 pix.
= 264.648 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1027 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.03577551 - 1.6952474
Average (Standard dev.)0.0009962796 (±0.022800788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.648 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73460_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73460_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1

EntireName: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
Components
  • Complex: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Melanoma-associated antigen 3
    • Protein or peptide: AD01-VHH
    • Protein or peptide: vAB30 light chain
    • Protein or peptide: vAB30 heavy chain

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Supramolecule #1: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1

SupramoleculeName: TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.73407 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 ...String:
GSHSMRYFFT SVSRPGRGEP RFIAVGYVDD TQFVRFDSDA ASQKMEPRAP WIEQEGPEYW DQETRNMKAH SQTDRANLGT LRGYYNQSE DGSHTIQIMY GCDVGPDGRF LRGYRQDAYD GKDYIALNED LRSWTAADMA AQITKRKWEA VHAAEQRRVY L EGRCVDGL RRYLENGKET LQRTDPPKTH MTHHPISDHE ATLRCWALGF YPAEITLTWQ RDGEDQTQDT ELVETRPAGD GT FQKWAAV VVPSGEEQRY TCHVQHEGLP KPLTLRWP

UniProtKB: MHC class I antigen

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Macromolecule #2: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 2 / 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 #3: Melanoma-associated antigen 3

MacromoleculeName: Melanoma-associated antigen 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.04315 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVDPIGHLY

UniProtKB: Melanoma-associated antigen 3

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Macromolecule #4: AD01-VHH

MacromoleculeName: AD01-VHH / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.449745 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVKLVESGGG LVQPGGSLRL SCAASGSIFS INTMGWYRQT PGKQRDLVAD ISSGGSTKYG DSVKGRFTIS RDNTKNTVYL QMNSLKPED TAVYYCYGLS YSNDDYWGQG TQVTVS

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Macromolecule #5: vAB30 light chain

MacromoleculeName: vAB30 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 22.793654 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGSIA DGYISWVRQA PGQGLEWMGG ILPRVQYTNY AQKFQGRVTI TADESTSTAY MELSSLRSE DTAVYYCARS PTATAAALKI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGSIA DGYISWVRQA PGQGLEWMGG ILPRVQYTNY AQKFQGRVTI TADESTSTAY MELSSLRSE DTAVYYCARS PTATAAALKI WGQGTMVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV

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Macromolecule #6: vAB30 heavy chain

MacromoleculeName: vAB30 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.497137 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPST LSASVGDRVT ITCRASRDIG RYLAWYQQKP GKAPKLLIYL SSSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYSIANQLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASVGDRVT ITCRASRDIG RYLAWYQQKP GKAPKLLIYL SSSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYSIANQLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TITAN THEMIS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1317109
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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