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Yorodumi- PDB-6bw3: Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bw3 | ||||||
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Title | Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide | ||||||
Components |
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Keywords | GENE REGULATION / NuRD / Complex / Epigenetics / Structural Genomics / Structural Genomics Consortium / SGC / Histone-binding protein / Chromatin regulator / Nucleus / Repressor / WD repeat | ||||||
Function / homology | Function and homology information CAF-1 complex / [histone H3]-lysine9 N-methyltransferase / heterochromatin organization / histone H3K9 methyltransferase activity / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex ...CAF-1 complex / [histone H3]-lysine9 N-methyltransferase / heterochromatin organization / histone H3K9 methyltransferase activity / NURF complex / NuRD complex / regulation of cell fate specification / DNA replication-dependent chromatin assembly / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by DREAM complex / ESC/E(Z) complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / negative regulation of JNK cascade / Polo-like kinase mediated events / negative regulation of programmed cell death / hematopoietic stem cell proliferation / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / histone deacetylase complex / G0 and Early G1 / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Deposition of new CENPA-containing nucleosomes at the centromere / Regulation of TP53 Activity through Acetylation / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / histone binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Oxidative Stress Induced Senescence / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / cell differentiation / regulation of cell cycle / nuclear speck / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / apoptotic process / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ivanochko, D. / Halabelian, L. / Hutchinson, A. / Seitova, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex. Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / ...Authors: Ivanochko, D. / Halabelian, L. / Henderson, E. / Savitsky, P. / Jain, H. / Marcon, E. / Duan, S. / Hutchinson, A. / Seitova, A. / Barsyte-Lovejoy, D. / Filippakopoulos, P. / Greenblatt, J. / Lima-Fernandes, E. / Arrowsmith, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bw3.cif.gz | 308.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bw3.ent.gz | 249.7 KB | Display | PDB format |
PDBx/mmJSON format | 6bw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/6bw3 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/6bw3 | HTTPS FTP |
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-Related structure data
Related structure data | 6bw4C 2xu7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 10 - 410 / Label seq-ID: 12 - 412
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-Components
#1: Protein | Mass: 47853.652 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBBP4, RBAP48 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09028 #2: Protein/peptide | Mass: 1379.699 Da / Num. of mol.: 2 / Fragment: N-terminal residues 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13465, UniProt: Q03112*PLUS #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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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: 2.34 Å3/Da / Density % sol: 47.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG3350, 0.2 M sodium malonate, 0.1 M BisTris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: May 10, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.2→46.95 Å / Num. obs: 46303 / % possible obs: 99.4 % / Redundancy: 4.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.056 / Rrim(I) all: 0.114 / Net I/σ(I): 14.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xu7 Resolution: 2.2→46.95 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.958 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.608 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→46.95 Å
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Refine LS restraints |
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