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Yorodumi- PDB-6w51: Structure of the antibody fragment H2 in complex with HLA-A*02:01... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w51 | ||||||
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Title | Structure of the antibody fragment H2 in complex with HLA-A*02:01/p53R175H | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunotherapy / MHC-I / HLA-A2 / p53 | ||||||
Function / homology | Function and homology information Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity ...Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / cellular response to actinomycin D / somitogenesis / type II interferon-mediated signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å | ||||||
Authors | Wright, K.M. / Gabelli, S.B. | ||||||
Citation | Journal: Science / Year: 2021 Title: Targeting a neoantigen derived from a common TP53 mutation. Authors: Hsiue, E.H. / Wright, K.M. / Douglass, J. / Hwang, M.S. / Mog, B.J. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Wang, Q. / Schaefer, A. / Miller, M.S. / Skora, A.D. / ...Authors: Hsiue, E.H. / Wright, K.M. / Douglass, J. / Hwang, M.S. / Mog, B.J. / Pearlman, A.H. / Paul, S. / DiNapoli, S.R. / Konig, M.F. / Wang, Q. / Schaefer, A. / Miller, M.S. / Skora, A.D. / Azurmendi, P.A. / Murphy, M.B. / Liu, Q. / Watson, E. / Li, Y. / Pardoll, D.M. / Bettegowda, C. / Papadopoulos, N. / Kinzler, K.W. / Vogelstein, B. / Gabelli, S.B. / Zhou, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w51.cif.gz | 638.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w51.ent.gz | 527.2 KB | Display | PDB format |
PDBx/mmJSON format | 6w51.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6w51_validation.pdf.gz | 577 KB | Display | wwPDB validaton report |
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Full document | 6w51_full_validation.pdf.gz | 660.1 KB | Display | |
Data in XML | 6w51_validation.xml.gz | 114.1 KB | Display | |
Data in CIF | 6w51_validation.cif.gz | 156.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/6w51 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w51 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ADGJBEHK
#1: Protein | Mass: 34183.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: U5YKE0 #2: Protein | Mass: 13732.547 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769 |
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-Protein/peptide , 1 types, 4 molecules CFIL
#3: Protein/peptide | Mass: 1114.320 Da / Num. of mol.: 4 / Mutation: R175H / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04637 |
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-Antibody , 2 types, 8 molecules MOQSNPRT
#4: Antibody | Mass: 23780.512 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #5: Antibody | Mass: 23698.314 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) |
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-Non-polymers , 2 types, 2 molecules
#6: Chemical | ChemComp-PO4 / |
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#7: 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: 2.46 Å3/Da / Density % sol: 49.95 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.2 M Ammonium chloride, 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.53→30.37 Å / Num. obs: 43734 / % possible obs: 95.3 % / Redundancy: 2.4 % / CC1/2: 0.938 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.186 / Rrim(I) all: 0.311 / Net I/σ(I): 3.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6O4Y, 6UJ9 Resolution: 3.53→30.37 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.823 / SU B: 43.916 / SU ML: 0.656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.816 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 245.65 Å2 / Biso mean: 61.859 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 3.53→30.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.53→3.618 Å / Rfactor Rfree error: 0
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