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Yorodumi- PDB-7z78: Crystal structure of compound 4 in complex with the bromodomain o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z78 | ||||||
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Title | Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and pVHL:ElonginC:ElonginB | ||||||
Components | Probable global transcription activator SNF2L2 | ||||||
Keywords | LIGASE / PROTAC / Complex / Bromodomain | ||||||
Function / homology | Function and homology information bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair ...bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / ATP-dependent chromatin remodeler activity / positive regulation of T cell differentiation / intermediate filament cytoskeleton / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / spermatid development / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / helicase activity / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / negative regulation of cell growth / RMTs methylate histone arginines / nervous system development / histone binding / transcription coactivator activity / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Bader, G. / Boettcher, J. / Wolkerstorfer, B. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo. Authors: Kofink, C. / Trainor, N. / Mair, B. / Wohrle, S. / Wurm, M. / Mischerikow, N. / Roy, M.J. / Bader, G. / Greb, P. / Garavel, G. / Diers, E. / McLennan, R. / Whitworth, C. / Vetma, V. / ...Authors: Kofink, C. / Trainor, N. / Mair, B. / Wohrle, S. / Wurm, M. / Mischerikow, N. / Roy, M.J. / Bader, G. / Greb, P. / Garavel, G. / Diers, E. / McLennan, R. / Whitworth, C. / Vetma, V. / Rumpel, K. / Scharnweber, M. / Fuchs, J.E. / Gerstberger, T. / Cui, Y. / Gremel, G. / Chetta, P. / Hopf, S. / Budano, N. / Rinnenthal, J. / Gmaschitz, G. / Mayer, M. / Koegl, M. / Ciulli, A. / Weinstabl, H. / Farnaby, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z78.cif.gz | 163.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z78.ent.gz | 128.5 KB | Display | PDB format |
PDBx/mmJSON format | 7z78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z78_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7z78_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7z78_validation.xml.gz | 19 KB | Display | |
Data in CIF | 7z78_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/7z78 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/7z78 | HTTPS FTP |
-Related structure data
Related structure data | 7z6lC 7z76C 7z77C 4qy4S 5t35S C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 14380.542 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Production host: Escherichia coli (E. coli) References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | ChemComp-ZN / #4: 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: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 8% ethylene glycol, 25% PEG 6000, 0.1 M HEPES pH 8.0 and 10 mM zinc chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→89.27 Å / Num. obs: 60981 / % possible obs: 94 % / Redundancy: 5.1 % / CC1/2: 0.999 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.324→1.347 Å / Num. unique obs: 51 / CC1/2: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T35, 4QY4 Resolution: 1.32→26.4 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.076 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.072
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Displacement parameters | Biso max: 255.41 Å2 / Biso mean: 29.14 Å2 / Biso min: 10.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.32→26.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.32→1.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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