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Yorodumi- PDB-4r8p: Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation m... -
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-Basic information
Entry | Database: PDB / ID: 4r8p | ||||||
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Title | Crystal structure of the Ring1B/Bmi1/UbcH5c PRC1 ubiquitylation module bound to the nucleosome core particle | ||||||
Components |
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Keywords | Structural Protein/DNA / RING domain / Arginine anchor / Ubiquitin ligase / Histone modification enzyme / Structural Protein-DNA complex | ||||||
Function / homology | Function and homology information histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis ...histone H2AK119 ubiquitin ligase activity / regulation of adaxial/abaxial pattern formation / rostrocaudal neural tube patterning / RING-like zinc finger domain binding / sex chromatin / PRC1 complex / segment specification / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / PcG protein complex / positive regulation of immature T cell proliferation in thymus / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K6-linked ubiquitination / Signaling by BMP / SUMOylation of DNA methylation proteins / protein K11-linked ubiquitination / gastrulation with mouth forming second / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / anterior/posterior axis specification / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression, epigenetic / : / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / ubiquitin conjugating enzyme activity / Transcriptional Regulation by E2F6 / protein monoubiquitination / germ cell development / MLL1 complex / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / negative regulation of BMP signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / heterochromatin / ubiquitin ligase complex / epigenetic regulation of gene expression / SUMOylation of DNA damage response and repair proteins / positive regulation of B cell proliferation / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / Negative regulators of DDX58/IFIH1 signaling / promoter-specific chromatin binding / apoptotic signaling pathway / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / brain development / protein modification process / euchromatin / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / negative regulation of DNA-binding transcription factor activity / protein polyubiquitination / structural constituent of chromatin / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of fibroblast proliferation / nucleosome / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / gene expression / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / protein ubiquitination / nuclear body / endosome membrane / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA repair / apoptotic process / chromatin binding / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) Synthetic DNA (others) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2846 Å | ||||||
Authors | McGinty, R.K. / Henrici, R.C. / Tan, S. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Authors: McGinty, R.K. / Henrici, R.C. / Tan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r8p.cif.gz | 905.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r8p.ent.gz | 737.8 KB | Display | PDB format |
PDBx/mmJSON format | 4r8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r8p ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r8p | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 6 types, 12 molecules AEBFCGDHKMLN
#1: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H3.2 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: histone H2B 1.1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281 #7: Protein | Mass: 12595.749 Da / Num. of mol.: 2 / Fragment: Residues 2-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMI1, PCGF4, RNF51 / Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P35226 #8: Protein | Mass: 30118.637 Da / Num. of mol.: 2 Fragment: Residues 2-116 of Ring1B and Residues 2-148 of UbcH5c Source method: isolated from a genetically manipulated source Details: Ring1B(2-116) fragment linked to UBE2D3/UbcH5c (2-148) through a linker encodin g the GSGSRS sequence Source: (gene. exp.) Homo sapiens (human) Gene: BAP1, DING, HIPI3, RING1B, Ring1B-UbcH5c fusion, RNF2, UBC5C, UBCH5C, UBE2D3 Plasmid: pST44 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: Q99496, UniProt: P61077, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases), ubiquitin-protein ligase |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45138.770 Da / Num. of mol.: 1 / Fragment: Widom 601 147-mer (+ strand) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic DNA (others) / Gene: Widom 601 nucleosome positioning sequence / Plasmid: pST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 |
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#6: DNA chain | Mass: 45610.043 Da / Num. of mol.: 1 / Fragment: Widom 601 147-mer (- strand) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synthetic DNA (others) / Gene: Widom 601 nucleosome positioning sequence / Plasmid: pST55 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 |
-Non-polymers , 1 types, 8 molecules
#9: Chemical | ChemComp-ZN / |
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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: 3.12 Å3/Da / Density % sol: 60.53 % |
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Crystal grow | Temperature: 294 K / Method: modified micro batch under oil / pH: 7.5 Details: 25 mM HEPES pH 7.5, 80 mM NH4NO3, 3 % PEG2000-MME, Modified micro batch under oil, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2846→45 Å / Num. all: 54219 / Num. obs: 54142 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.9 % / Biso Wilson estimate: 105.01 Å2 / Rsym value: 0.063 / Net I/σ(I): 16.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polyalanine models of PDB entries 3RPG and 3LZ0 Resolution: 3.2846→45 Å / SU ML: 0.43 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.77 / 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: 368.24 Å2 / Biso mean: 137.4911 Å2 / Biso min: 44.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2846→45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 29.28 Å / Origin y: 30.3205 Å / Origin z: -47.343 Å
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Refinement TLS group |
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