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Yorodumi- PDB-5wai: Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wai | ||||||
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Title | Crystal Structure of a Suz12-Rbbp4-Jarid2-Aebp2 Heterotetrameric Complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Methyltransferase | ||||||
Function / homology | Function and homology information protein localization to pericentric heterochromatin / sex chromatin / CAF-1 complex / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / facultative heterochromatin formation / NURF complex ...protein localization to pericentric heterochromatin / sex chromatin / CAF-1 complex / random inactivation of X chromosome / ubiquitin-modified histone reader activity / histone H3K27 methyltransferase activity / negative regulation of cardiac muscle hypertrophy / negative regulation of cardiac muscle cell proliferation / facultative heterochromatin formation / 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 / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / Polo-like kinase mediated events / lncRNA binding / cardiac muscle cell proliferation / histone methyltransferase complex / ATPase complex / G1/S-Specific Transcription / Sin3-type complex / positive regulation of stem cell population maintenance / histone methyltransferase activity / oligodendrocyte differentiation / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / negative regulation of cell differentiation / histone deacetylase complex / G0 and Early G1 / enzyme activator activity / 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 / spleen development / methylated histone binding / Regulation of TP53 Activity through Acetylation / cellular response to leukemia inhibitory factor / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / thymus development / liver development / PRC2 methylates histones and DNA / ubiquitin binding / Regulation of PTEN gene transcription / central nervous system development / Defective pyroptosis / promoter-specific chromatin binding / HDACs deacetylate histones / stem cell differentiation / transcription coregulator activity / negative regulation of transforming growth factor beta receptor signaling pathway / brain development / chromatin DNA binding / PKMTs methylate histone lysines / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / histone deacetylase binding / chromatin organization / histone binding / regulation of gene expression / Oxidative Stress Induced Senescence / cell population proliferation / Potential therapeutics for SARS / DNA replication / chromosome, telomeric region / nuclear body / chromatin remodeling / cell cycle / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / 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-containing complex / mitochondrion / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Neovison vison (American mink) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Chen, S. / Jiao, L. / Liu, X. | ||||||
Citation | Journal: Mol. Cell / Year: 2018 Title: Unique Structural Platforms of Suz12 Dictate Distinct Classes of PRC2 for Chromatin Binding. Authors: Chen, S. / Jiao, L. / Shubbar, M. / Yang, X. / Liu, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wai.cif.gz | 673.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wai.ent.gz | 547.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/5wai ftp://data.pdbj.org/pub/pdb/validation_reports/wa/5wai | HTTPS FTP |
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-Related structure data
Related structure data | 5wakC 3gfcS 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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-Components
#1: Protein | Mass: 49367.398 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 | Mass: 55686.227 Da / Num. of mol.: 2 / Fragment: UNP residues 76-545 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022 #3: Protein | Mass: 11592.598 Da / Num. of mol.: 2 / Fragment: UNP residues 191-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AEBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZN18 #4: Protein/peptide | Mass: 2257.717 Da / Num. of mol.: 2 / Fragment: UNP residues 39-57 / Source method: obtained synthetically / Source: (synth.) Neovison vison (American mink) / References: UniProt: U6DXQ8, UniProt: Q92833*PLUS #5: Chemical | |
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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: 2.83 Å3/Da / Density % sol: 61.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% PEG6000, 5%v/v(+/-)-2-Methyl-2,4-pentaneediol (MPD) and 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.1 Å / Num. obs: 67533 / % possible obs: 99.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 68.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.042 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 12.6 % / Rmerge(I) obs: 2.851 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2989 / CC1/2: 0.472 / Rpim(I) all: 0.828 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GFC Resolution: 2.9→48.1 Å / Cor.coef. Fo:Fc: 0.9356 / Cor.coef. Fo:Fc free: 0.8975 / SU R Cruickshank DPI: 0.777 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.685 / SU Rfree Blow DPI: 0.295 / SU Rfree Cruickshank DPI: 0.303
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Displacement parameters | Biso mean: 66.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.9→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.98 Å / 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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