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Yorodumi- PDB-7pdw: Crystal structure of parent TCR (728) complexed to HLA-A*02:01 pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pdw | ||||||
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Title | Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / T-cell receptor / human leukocyte antigen / MAGE-A10 | ||||||
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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / 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 / histone deacetylase binding / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / 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 / 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 / ER-Phagosome pathway / iron ion transport / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Simister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J Immunother Cancer / Year: 2022 Title: Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy. Authors: Simister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pdw.cif.gz | 636.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pdw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pdw_validation.pdf.gz | 493.7 KB | Display | wwPDB validaton report |
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Full document | 7pdw_full_validation.pdf.gz | 504.7 KB | Display | |
Data in XML | 7pdw_validation.xml.gz | 62.2 KB | Display | |
Data in CIF | 7pdw_validation.cif.gz | 88.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/7pdw ftp://data.pdbj.org/pub/pdb/validation_reports/pd/7pdw | HTTPS FTP |
-Related structure data
Related structure data | 7pbcSC 7pdxC 7qpjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-T-cell receptor ... , 2 types, 4 molecules AAAFFFBBBGGG
#1: Protein | Mass: 22818.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 27185.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Protein , 2 types, 4 molecules DDDIIICCCHHH
#3: Protein | Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 #5: Protein | Mass: 32082.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7 |
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-Protein/peptide , 1 types, 2 molecules EEEJJJ
#4: Protein/peptide | Mass: 1035.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Melanoma-associated antigen 10 / Source: (synth.) Homo sapiens (human) / References: UniProt: P43363 |
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-Non-polymers , 3 types, 647 molecules
#6: Chemical | ChemComp-PO4 / | ||
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#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6572 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.02M Sodium/potassium phosphate, 0.1M Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.82→98.71 Å / Num. obs: 158062 / % possible obs: 90.2 % / Redundancy: 1.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.098 / Rrim(I) all: 0.139 / Net I/σ(I): 4.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7PBC Resolution: 1.82→81.936 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.004 / SU ML: 0.136 / Cross valid method: FREE R-VALUE / ESU R: 0.147 / ESU R Free: 0.133 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→81.936 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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