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- PDB-33ci: Cryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in compl... -

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Basic information

Entry
Database: PDB / ID: 33ci
TitleCryo-EM structure of MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58
Components
  • Beta-2-microglobulin
  • Fab BBM.1 heavy chain
  • Fab BBM.1 light chain
  • Fab VR-6 heavy chain
  • Fab VR-6 light chain
  • MHC class I antigen
  • Melanoma-associated antigen 4
KeywordsIMMUNE SYSTEM / HLA / MHC / antibody
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsSchuster, S. / Weng, T.-H. / Reinhart, C. / Michel, H. / Birkenfeld, J.
Funding support Germany, 1items
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, F.A. / 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. / ...Authors: Schuster, S. / Hartl, F.A. / 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, B.K.Q. / Link, S. / Goll, J. / Leoni, B. / Steinmann, B. / Selinger, O. / Welsch, S. / Roth, G. / Michel, H. / Klatt, M. / Birkenfeld, J.
History
DepositionAug 9, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Melanoma-associated antigen 4
F: Fab BBM.1 light chain
G: Fab BBM.1 heavy chain
D: Fab VR-6 light chain
E: Fab VR-6 heavy chain


Theoretical massNumber of molelcules
Total (without water)146,7937
Polymers146,7937
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 34155.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Avi-tag / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F6IQS1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Antibody , 4 types, 4 molecules FGDE

#4: Antibody Fab BBM.1 light chain


Mass: 23338.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The cryo-EM density for the constant region (111-216) is not well-resolved and thus the atomic model was not built.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody Fab BBM.1 heavy chain


Mass: 23627.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The cryo-EM density for the constant region (121-224) is not well-resolved and thus the atomic model was not built.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#6: Antibody Fab VR-6 light chain


Mass: 22847.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The cryo-EM density for the constant region (112-218) is not well-resolved and thus the atomic model was not built.
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#7: Antibody Fab VR-6 heavy chain


Mass: 29811.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The cryo-EM density for the constant region (121-276) is not well-resolved and thus the atomic model was not built.
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Protein/peptide / Non-polymers , 2 types, 8 molecules C

#3: Protein/peptide Melanoma-associated antigen 4 / Cancer/testis antigen 1.4 / CT1.4 / MAGE-4 antigen / MAGE-41 antigen / MAGE-X2 antigen


Mass: 1134.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43358
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MAGE-A4 (230-239)-bound HLA-A*02:01 in complex with Fab VR-58
Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.3
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2cryoSPARCparticle selection
3PHENIX1.20.1_4487model refinement
6cryoSPARCCTF correction
11cryoSPARCinitial Euler assignment
12cryoSPARCfinal Euler assignment
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3126711
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 605745 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Accession code: 33CG / Initial refinement model-ID: 1 / PDB-ID: 33CG

33cg

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1AA
2BB
3CC
4FF
5GG
RefinementHighest resolution: 2.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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