+Open data
-Basic information
Entry | Database: PDB / ID: 7usi | ||||||
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Title | BRD2-BD1 in complex with MDP5 | ||||||
Components | Bromodomain-containing protein 2BRD2 | ||||||
Keywords | TRANSCRIPTON/INHIBITOR / Inhibitor / acetyllysine binding pocket / TRANSCRIPTON-INHIBITOR complex | ||||||
Function / homology | Function and homology information chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Jayasinghe, T.D. / Ronning, D.R. | ||||||
Funding support | 1items
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Citation | Journal: J Control Release / Year: 2023 Title: Targeting BRD4 and PI3K signaling pathways for the treatment of medulloblastoma. Authors: Sethi, B. / Kumar, V. / Jayasinghe, T.D. / Dong, Y. / Ronning, D.R. / Zhong, H.A. / Coulter, D.W. / Mahato, R.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7usi.cif.gz | 158.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7usi.ent.gz | 126.6 KB | Display | PDB format |
PDBx/mmJSON format | 7usi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/us/7usi ftp://data.pdbj.org/pub/pdb/validation_reports/us/7usi | HTTPS FTP |
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-Related structure data
Related structure data | 7usgC 7ushC 7usjC 7uskC 6jkeS 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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2 |
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3 |
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5 |
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6 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 13504.795 Da / Num. of mol.: 6 / Fragment: BD1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440 |
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-Non-polymers , 8 types, 131 molecules
#2: Chemical | ChemComp-O6O / ( #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-CL / #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
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-Details
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: 3.49 Å3/Da / Density % sol: 64.71 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Sodium tartrate dibasic dihydrate pH 7.5 and 20 % w/v PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→35.56 Å / Num. obs: 38336 / % possible obs: 99.69 % / Redundancy: 6.9 % / CC1/2: 0.978 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.048 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 3871 / CC1/2: 0.834 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JKE Resolution: 2.5→35.56 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.32 Å2 / Biso mean: 55.3215 Å2 / Biso min: 30.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→35.56 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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