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- PDB-9ytd: Designed antibody vAB66 targeting PAP-HLA A*02:01 -

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Basic information

Entry
Database: PDB / ID: 9ytd
TitleDesigned antibody vAB66 targeting PAP-HLA A*02:01
Components
  • AD01 nanobody
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Prostatic acid phosphatase-derived peptide
  • vAB66 heavy chain
  • vAB66 light chain
KeywordsDE NOVO PROTEIN/IMMUNE SYSTEM / Fab / complex / immunology / DE NOVO PROTEIN / DE NOVO PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / dephosphorylation / vesicle membrane / azurophil granule membrane / phosphatase activity / purine nucleobase metabolic process / antigen processing and presentation of peptide antigen via MHC class I / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / 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 / filopodium / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 erythrocyte differentiation / regulation of iron ion transport / 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 / lipid metabolic process / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / apical part of cell / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / molecular adaptor activity / 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 / nucleus / membrane
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / 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 / Prostatic acid phosphatase / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsJude, K.M. / Garcia, K.C.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)OT2CA297242 United States
Cancer Research UKCGCATF-2023/100006 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103867 08 United States
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Primary map / Data content type: Primary map / 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: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Prostatic acid phosphatase-derived peptide
D: AD01 nanobody
H: vAB66 heavy chain
L: vAB66 light chain


Theoretical massNumber of molelcules
Total (without water)105,7926
Polymers105,7926
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / HLA A*02:01


Mass: 32256.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Met1 is a cloning artifact / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A5I8L1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Details: Met1 is a cloning artifact / Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Antibody , 3 types, 3 molecules DHL

#4: Antibody AD01 nanobody


Mass: 13867.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: Antibody vAB66 heavy chain


Mass: 23158.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#6: Antibody vAB66 light chain


Mass: 23649.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)

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Protein/peptide / Non-polymers , 2 types, 65 molecules C

#3: Protein/peptide Prostatic acid phosphatase-derived peptide / PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine ...PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine phosphatase ACP3 / Thiamine monophosphatase / TMPase


Mass: 981.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P15309, acid phosphatase, 5'-nucleotidase, protein-tyrosine-phosphatase
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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

Component
IDNameTypeEntity IDParent-IDSource
1vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducialCOMPLEX#1-#60MULTIPLE SOURCES
2HLA A*02:01 displaying PAP peptideCOMPLEX#1-#31MULTIPLE SOURCES
3vAB66 FabCOMPLEX#5-#61RECOMBINANT
4HLA A*02:01COMPLEX#1-#22RECOMBINANT
5PAP peptideCOMPLEX#32SYNTHETIC
6AD01 nanobodyCOMPLEX#41RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11.105260 MDaNO
22.045018 MDaNO
33.046394 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23synthetic construct (others)32630
24Homo sapiens (human)9606
35Homo sapiens (human)9606
46Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
23Cricetulus griseus (Chinese hamster)10029
24Escherichia coli (E. coli)562
36Homo sapiens (human)9606
Buffer solutionpH: 7.3
Buffer component
IDConc.NameFormulaBuffer-ID
10.15 Msodium chlorideNaCl1
20.01 MHEPES1
30.01 vol %fluorinated octyl maltoside1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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 magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5.893 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12293
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 6 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
4cryoSPARC4.6.2CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.6.2initial Euler assignment
10cryoSPARC4.6.2final Euler assignment
11cryoSPARC4.6.2classification
12cryoSPARC4.6.23D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionDetails: patch correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6762787 / Details: template picks based on 2D-classified blob picks
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 880830 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17YV1

7yv1

17YV11PDBexperimental model
23SOB

3sob

13SOB2PDBexperimental model
37SRO

7sro
PDB Unreleased entry

17SRO3PDBexperimental model
49NMV

9nmv
PDB Unreleased entry

19NMV4PDBexperimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00257488
ELECTRON MICROSCOPYf_angle_d0.527410176
ELECTRON MICROSCOPYf_chiral_restr0.04261100
ELECTRON MICROSCOPYf_plane_restr0.00471310
ELECTRON MICROSCOPYf_dihedral_angle_d12.01872704

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