+Open data
-Basic information
Entry | Database: PDB / ID: 8fvs | ||||||
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Title | Bromodomain of CBP liganded with CCS1477int | ||||||
Components | Histone acetyltransferase | ||||||
Keywords | TRANSFERASE / bromodomain / complex / TRANSCRIPTION | ||||||
Function / homology | Function and homology information histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / chromatin DNA binding / transcription regulator complex / transcription coactivator activity / nuclear body / positive regulation of transcription by RNA polymerase II / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Schonbrunn, E. / Bikowitz, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Group 3 medulloblastoma transcriptional networks collapse under domain specific EP300/CBP inhibition. Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / ...Authors: Shendy, N.A.M. / Bikowitz, M. / Sigua, L.H. / Zhang, Y. / Mercier, A. / Khashana, Y. / Nance, S. / Liu, Q. / Delahunty, I.M. / Robinson, S. / Goel, V. / Rees, M.G. / Ronan, M.A. / Wang, T. / Kocak, M. / Roth, J.A. / Wang, Y. / Freeman, B.B. / Orr, B.A. / Abraham, B.J. / Roussel, M.F. / Schonbrunn, E. / Qi, J. / Durbin, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fvs.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fvs.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fvs_validation.pdf.gz | 982.2 KB | Display | wwPDB validaton report |
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Full document | 8fvs_full_validation.pdf.gz | 986.5 KB | Display | |
Data in XML | 8fvs_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8fvs_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvs ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvs | HTTPS FTP |
-Related structure data
Related structure data | 8fv2C 8fvfC 8fvkC 8fxaC 8fxeC 8fxoC 8g6tC 8ga2C 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: 13847.882 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: I3L466, histone acetyltransferase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.31 Å3/Da / Density % sol: 46.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1 M Tris 8.5, 25 % w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→39.79 Å / Num. obs: 25279 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.244 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.75→1.8 Å / Mean I/σ(I) obs: 6.1 / Num. unique obs: 1817 / CC1/2: 0.931 / Rrim(I) all: 0.574 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→39.79 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→39.79 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 1.0762 Å / Origin y: -3.8265 Å / Origin z: -11.4598 Å
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Refinement TLS group | Selection details: all |