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- PDB-7tr4: MA2-MART1-HLAA0201 -

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Basic information

Entry
Database: PDB / ID: 7tr4
TitleMA2-MART1-HLAA0201
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA-A*02:01
  • Heavy chain
  • Light chain
  • Melanoma antigen recognized by T-cells 1
KeywordsIMMUNE SYSTEM / TCRm antibody MART1 HLA-A2
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / trans-Golgi network / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / melanosome / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Protein melan-A / Protein melan-A / Beta-2-Microglobulin / 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 ...Protein melan-A / Protein melan-A / Beta-2-Microglobulin / 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
Beta-2-microglobulin / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYang, X. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI103867-08 United States
CitationJournal: Nat.Biotechnol. / Year: 2023
Title: Facile repurposing of peptide-MHC-restricted antibodies for cancer immunotherapy.
Authors: Yang, X. / Nishimiya, D. / Lochte, S. / Jude, K.M. / Borowska, M. / Savvides, C.S. / Dougan, M. / Su, L. / Zhao, X. / Piehler, J. / Garcia, K.C.
History
DepositionJan 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A*02:01
B: Beta-2-microglobulin
H: Light chain
L: Heavy chain
P: Melanoma antigen recognized by T-cells 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8468
Polymers90,5695
Non-polymers2763
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-53 kcal/mol
Surface area36350 Å2
Unit cell
Length a, b, c (Å)267.190, 46.498, 78.513
Angle α, β, γ (deg.)90.000, 99.670, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA-A*02:01


Mass: 32125.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11635.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide Melanoma antigen recognized by T-cells 1 / MART-1 / Antigen LB39-AA / Antigen SK29-AA / Protein Melan-A


Mass: 985.176 Da / Num. of mol.: 1 / Fragment: residues 26-35 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655

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Antibody , 2 types, 2 molecules HL

#3: Antibody Light chain /


Mass: 22863.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Antibody Heavy chain


Mass: 22960.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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Non-polymers , 2 types, 113 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG-6000 0.1M Tris (pH8) 0.2M MgCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→46.45 Å / Num. obs: 42458 / % possible obs: 98.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 39.94 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 2605 / CC1/2: 0.428

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJF

3gjf


Resolution: 2.3→46.45 Å / SU ML: 0.3569 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.267 1997 4.71 %
Rwork0.2234 40427 -
obs0.2254 42424 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 18 110 6361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00146411
X-RAY DIFFRACTIONf_angle_d0.46128733
X-RAY DIFFRACTIONf_chiral_restr0.0396948
X-RAY DIFFRACTIONf_plane_restr0.00371131
X-RAY DIFFRACTIONf_dihedral_angle_d10.51132270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3871170.32852405X-RAY DIFFRACTION83.23
2.36-2.420.32621430.3142891X-RAY DIFFRACTION99.8
2.42-2.490.35241430.29182876X-RAY DIFFRACTION99.83
2.49-2.570.33941430.28432916X-RAY DIFFRACTION99.71
2.57-2.660.29861430.27342874X-RAY DIFFRACTION99.77
2.66-2.770.36121440.28122928X-RAY DIFFRACTION99.68
2.77-2.890.31951440.28592916X-RAY DIFFRACTION99.74
2.89-3.050.34531430.26762888X-RAY DIFFRACTION99.7
3.05-3.240.29381430.24982903X-RAY DIFFRACTION99.9
3.24-3.490.23151460.23292929X-RAY DIFFRACTION99.9
3.49-3.840.2671440.20642927X-RAY DIFFRACTION99.77
3.84-4.390.25641460.17422948X-RAY DIFFRACTION99.58
4.39-5.530.18911460.16352956X-RAY DIFFRACTION99.74
5.54-46.450.22311520.19693070X-RAY DIFFRACTION99.54

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