+Open data
-Basic information
Entry | Database: PDB / ID: 8d5e | ||||||
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Title | The complex of Gtf2b Peptide TGAASFDEF Presented by H2-Dd | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complex / MHC | ||||||
Function / homology | Function and homology information RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / positive regulation of core promoter binding / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / TAP1 binding ...RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Pre-transcription Events / positive regulation of core promoter binding / RNA polymerase II core complex assembly / transcriptional start site selection at RNA polymerase II promoter / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / nuclear thyroid hormone receptor binding / transcription preinitiation complex / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / transcription factor TFIID complex / positive regulation of natural killer cell mediated cytotoxicity / protein acetylation / RNA polymerase II general transcription initiation factor activity / regulation of membrane depolarization / RNA polymerase II complex binding / viral transcription / acetyltransferase activity / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / positive regulation of immunoglobulin production / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / positive regulation of interleukin-4 production / RNA polymerase II core promoter sequence-specific DNA binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / protection from natural killer cell mediated cytotoxicity / histone acetyltransferase / negative regulation of T cell proliferation / 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 / TBP-class protein binding / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / promoter-specific chromatin binding / protein-DNA complex / lumenal side of endoplasmic reticulum membrane / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / RNA polymerase II transcription regulator complex Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Custodio, J.M.F. / Baker, B.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Structural and physical features that distinguish tumor-controlling from inactive cancer neoepitopes. Authors: Custodio, J.M. / Ayres, C.M. / Rosales, T.J. / Brambley, C.A. / Arbuiso, A.G. / Landau, L.M. / Keller, G.L.J. / Srivastava, P.K. / Baker, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d5e.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d5e.ent.gz | 134.6 KB | Display | PDB format |
PDBx/mmJSON format | 8d5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5e ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5e | HTTPS FTP |
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-Related structure data
Related structure data | 8d5fC 8d5kC 5kd7S 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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-Components
#1: Protein | Mass: 31876.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pMBIO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01900 |
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#2: Protein | Mass: 11791.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887 |
#3: Protein/peptide | Mass: 943.953 Da / Num. of mol.: 1 / Fragment: UNP residues 88-96 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P62915, histone acetyltransferase |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | Temperature: 309.15 K / Method: vapor diffusion, hanging drop / Details: 15% w/v PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.46→47.391 Å / Num. obs: 16346 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.988 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.084 / Rrim(I) all: 0.208 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 5.7 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5KD7 Resolution: 2.46→47.391 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.191 / SU B: 18.284 / SU ML: 0.202 / Average fsc free: 0.9542 / Average fsc work: 0.9711 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.276 / Details: Hydrogens have not been used
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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: 38.695 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→47.391 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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