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- EMDB-59343: Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-59343
TitleCryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4
Map data
Sample
  • Complex: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Melanoma-associated antigen 4
    • Protein or peptide: Fab BBM.1 light chain
    • Protein or peptide: Fab BBM.1 heavy chain
    • Protein or peptide: Fab VR-4 light chain
    • Protein or peptide: Fab VR-4 heavy chain
  • Ligand: water
KeywordsHLA / MHC / antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / positive regulation of cell cycle / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport ...antigen processing and presentation of peptide antigen via MHC class I / positive regulation of cell cycle / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / histone deacetylase binding / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / lysosomal membrane / negative regulation of apoptotic process / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / negative regulation of transcription by RNA polymerase II / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane
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 4 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsSchuster S / Weng T-H / Reinhart C / Michel H / Birkenfeld J
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Systematic De-Risking of TCR-Mimic Therapeutics Through Proteome-Wide Off-Target Landscaping and a Generalizable Design Rule Framework
Authors: Schuster S / Hartl FA / Stehle J / Beier F / Al-Hasani H / Reinhart C / Weng T-H / Kraemer S / Hamde P / Herz T / Oesterlin S / Schmidt M / Gross T / Stehl L / Kilb N / Juenemann G / Heiss K ...Authors: Schuster S / Hartl FA / Stehle J / Beier F / Al-Hasani H / Reinhart C / Weng T-H / Kraemer S / Hamde P / Herz T / Oesterlin S / Schmidt M / Gross T / Stehl L / Kilb N / Juenemann G / Heiss K / Sinclair A / Schoettgen J / Meyer P / Atay B / Zaghla BKQ / Link S / Goll J / Leoni B / Steinmann B / Selinger O / Welsch S / Roth G / Michel H / Klatt M / Birkenfeld J
History
DepositionAug 9, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59343.png

Downloads & links

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Map

FileDownload / File: emd_59343.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 360 pix.
= 288.792 Å		0.8 Å/pix.
x 360 pix.
= 288.792 Å		0.8 Å/pix.
x 360 pix.
= 288.792 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8022 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.49330866 - 0.7825748
Average (Standard dev.)0.00015933886 (±0.009856699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 288.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59343_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_59343_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_59343_half_map_2.map
Projections & Slices
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Sample components

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Entire : MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6

EntireName: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
Components
  • Complex: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
    • Protein or peptide: MHC class I antigen
    • Protein or peptide: Beta-2-microglobulin
    • Protein or peptide: Melanoma-associated antigen 4
    • Protein or peptide: Fab BBM.1 light chain
    • Protein or peptide: Fab BBM.1 heavy chain
    • Protein or peptide: Fab VR-4 light chain
    • Protein or peptide: Fab VR-4 heavy chain
  • Ligand: water

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Supramolecule #1: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6

SupramoleculeName: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: MHC class I antigen

MacromoleculeName: MHC class I antigen / type: protein_or_peptide / ID: 1 / Details: C-terminal Avi-tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.155773 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGCYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM CAQTTKHKWE AAHVAEQLRA Y LEGTCVEW ...String:
MGSHSMRYFF TSVSRPGRGE PRFIAVGYVD DTQFVRFDSD AASQRMEPRA PWIEQEGPEY WDGETRKVKA HSQTHRVDLG TLRGCYNQS EAGSHTVQRM YGCDVGSDWR FLRGYHQYAY DGKDYIALKE DLRSWTAADM CAQTTKHKWE AAHVAEQLRA Y LEGTCVEW LRRYLENGKE TLQRTDAPKT HMTHHAVSDH EATLRCWALS FYPAEITLTW QRDGEDQTQD TELVETRPAG DG TFQKWAA VVVPSGQEQR YTCHVQHEGL PKPLTLRWEP GSGSGLNDIF EAQKIEWHE

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: Escherichia coli BL21(DE3) (bacteria)
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 4

MacromoleculeName: Melanoma-associated antigen 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.1342 KDa
SequenceString:
GVYDGREHTV

UniProtKB: Melanoma-associated antigen 4

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Macromolecule #4: Fab BBM.1 light chain

MacromoleculeName: Fab BBM.1 light chain / type: protein_or_peptide / ID: 4
Details: The cryo-EM density for the constant region (111-216) is not well-resolved and thus the atomic model was not built.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.338051 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIQMTQSPAS QSASLGESVT ITCLASQTIG TWLAWYQQKP GKSPQLLIYA ATSLADGVPS RFSGSGSGTK FSLKIRTLQA EDFVSYYCQ QLYSKPYTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS QSASLGESVT ITCLASQTIG TWLAWYQQKP GKSPQLLIYA ATSLADGVPS RFSGSGSGTK FSLKIRTLQA EDFVSYYCQ QLYSKPYTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #5: Fab BBM.1 heavy chain

MacromoleculeName: Fab BBM.1 heavy chain / type: protein_or_peptide / ID: 5
Details: The cryo-EM density for the constant region (121-224) is not well-resolved and thus the atomic model was not built.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.627389 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLQQSGAE LVKPGASVKL SCTPSGFNVK DTYIHWVKQR PKQGLEWIGR IDPSDGDIKY DPKFQGKATI TADTSSNTVS LQLSSLTSE DTAVYYCARW FGDYGAMNYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
EVQLQQSGAE LVKPGASVKL SCTPSGFNVK DTYIHWVKQR PKQGLEWIGR IDPSDGDIKY DPKFQGKATI TADTSSNTVS LQLSSLTSE DTAVYYCARW FGDYGAMNYW GQGTSVTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSC

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Macromolecule #6: Fab VR-4 light chain

MacromoleculeName: Fab VR-4 light chain / type: protein_or_peptide / ID: 6
Details: The cryo-EM density for the constant region (113-218) is not well-resolved and thus the atomic model was not built.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.747256 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIVMTQSPSS LSASVGDRVT ITCQASQDIN NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISSLQP EDIATYFCQ QYDNLPRSIT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
DIVMTQSPSS LSASVGDRVT ITCQASQDIN NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISSLQP EDIATYFCQ QYDNLPRSIT FGQGTRLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #7: Fab VR-4 heavy chain

MacromoleculeName: Fab VR-4 heavy chain / type: protein_or_peptide / ID: 7
Details: The cryo-EM density for the constant region (121-275) is not well-resolved and thus the atomic model was not built.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.592916 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGPG LVKPSGTLSL TCAVSGVSIS SNKWWNWVRQ PPGKGLEWIG EVYHSGSTNY NPSLKSRVTI SVDKSKNQFS LRLSSVTAA DTAVYYCARD YSNYGFDYWG QGALVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLVQSGPG LVKPSGTLSL TCAVSGVSIS SNKWWNWVRQ PPGKGLEWIG EVYHSGSTNY NPSLKSRVTI SVDKSKNQFS LRLSSVTAA DTAVYYCARD YSNYGFDYWG QGALVTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCAAAEQKL ISEEDLNEME QK LISEEDL NEMEQKLISE EDLNEMAAHH HHHHHH

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration0.5 mg/mL
BufferpH: 7.3
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2403407
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 349805
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

33cg

chain_id: A, source_name: PDB, initial_model_type: experimental model

33cg

chain_id: B, source_name: PDB, initial_model_type: experimental model

33cg

chain_id: C, source_name: PDB, initial_model_type: experimental model

33cg

chain_id: F, source_name: PDB, initial_model_type: experimental model

33cg

chain_id: G, source_name: PDB, initial_model_type: experimental model
SoftwareName: ISOLDE
Output model

PDB-33ch:
Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-4

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