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Yorodumi- PDB-5epl: Crystal Structure of chromodomain of CBX4 in complex with inhibit... -
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-Basic information
Entry | Database: PDB / ID: 5epl | |||||||||
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Title | Crystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866 | |||||||||
Components |
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Keywords | transcription/transcription inhibitor / structural genomics / Structural Genomics Consortium / SGC / transcription-transcription inhibitor complex | |||||||||
Function / homology | Function and homology information PRC1 complex / SUMO ligase activity / PcG protein complex / SUMO binding / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known ...PRC1 complex / SUMO ligase activity / PcG protein complex / SUMO binding / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / SUMOylation of chromatin organization proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / protein sumoylation / SUMOylation of DNA damage response and repair proteins / Regulation of PTEN gene transcription / methylated histone binding / SUMOylation of transcription cofactors / phosphoprotein binding / transcription corepressor activity / chromatin organization / Oxidative Stress Induced Senescence / transcription cis-regulatory region binding / single-stranded RNA binding / nuclear body / nuclear speck / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å | |||||||||
Authors | Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Liu, Y. / Tempel, W. / Walker, J.R. / Stuckey, J.I. / Dickson, B.M. / James, L.I. / Frye, S.V. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Authors: Stuckey, J.I. / Dickson, B.M. / Cheng, N. / Liu, Y. / Norris, J.L. / Cholensky, S.H. / Tempel, W. / Qin, S. / Huber, K.G. / Sagum, C. / Black, K. / Li, F. / Huang, X.P. / Roth, B.L. / ...Authors: Stuckey, J.I. / Dickson, B.M. / Cheng, N. / Liu, Y. / Norris, J.L. / Cholensky, S.H. / Tempel, W. / Qin, S. / Huber, K.G. / Sagum, C. / Black, K. / Li, F. / Huang, X.P. / Roth, B.L. / Baughman, B.M. / Senisterra, G. / Pattenden, S.G. / Vedadi, M. / Brown, P.J. / Bedford, M.T. / Min, J. / Arrowsmith, C.H. / James, L.I. / Frye, S.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5epl.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5epl.ent.gz | 51.9 KB | Display | PDB format |
PDBx/mmJSON format | 5epl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5epl_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 5epl_full_validation.pdf.gz | 437.3 KB | Display | |
Data in XML | 5epl_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 5epl_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5epl ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5epl | HTTPS FTP |
-Related 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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Details | AUTHORS HAVE NOT INDICATED THE BIOLOGICAL UNIT |
-Components
#1: Protein | Mass: 7354.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBX4 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 References: UniProt: O00257, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Protein/peptide | #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: 2.7 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 30% PEG3350, 0.2M sodium chloride, 0.1 M sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786036 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786036 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→44.35 Å / Num. obs: 16048 / % possible obs: 99.9 % / Redundancy: 20.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 19.6 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 5.4 / % possible all: 98.7 |
-Processing
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Refinement | Resolution: 1.81→44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.79 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH AN ISOMORPHOUS CRYSTAL, FOLLOWED BY PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING WITH ARP/WARP. PHENIX.ELBOW/MOGUL WAS USED TO ...Details: THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT WITH AN ISOMORPHOUS CRYSTAL, FOLLOWED BY PHASE IMPROVEMENT AND AUTOMATED MODEL BUILDING WITH ARP/WARP. PHENIX.ELBOW/MOGUL WAS USED TO GENERATE GEOMETRY RESTRAINTS FOR INHIBITOR BUILDING BLOCKS. LIGAND WAS USED FOR PREPARATION OF LINK RESTRAINTS. LINK RESTRAINTS WERE MANUALLY MODIFIED, FOR EXAMPLE TO ESTABLISH PLANAR GEOMETRY OF METHYL ESTER TERMINUS OF INHIBITOR. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.ELECTRON DENSITY DID NOT FULLY RESOLVE THE LIGAND'S C-TERMINAL SERINE ESTER MOIETY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→44 Å
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