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Yorodumi- PDB-6i2m: Crystal structure of vaccinia virus protein A55 BTB-Back domain i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i2m | ||||||||||||
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Title | Crystal structure of vaccinia virus protein A55 BTB-Back domain in complex with human Cullin-3 N-terminus | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / BTB-Kelch / Cul3 / vaccinia virus | ||||||||||||
Function / homology | Function and homology information : / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating ...: / liver morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / POZ domain binding / nuclear protein quality control by the ubiquitin-proteasome system / regulation protein catabolic process at postsynapse / polar microtubule / anaphase-promoting complex-dependent catabolic process / COPII vesicle coating / stem cell division / RHOBTB3 ATPase cycle / embryonic cleavage / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / Notch binding / RHOBTB1 GTPase cycle / fibroblast apoptotic process / negative regulation of Rho protein signal transduction / negative regulation of type I interferon production / ubiquitin ligase complex scaffold activity / mitotic metaphase chromosome alignment / Cul3-RING ubiquitin ligase complex / stress fiber assembly / positive regulation of cytokinesis / protein monoubiquitination / sperm flagellum / protein autoubiquitination / RHOBTB2 GTPase cycle / protein K48-linked ubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / gastrulation / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / integrin-mediated signaling pathway / Degradation of DVL / cellular response to amino acid stimulus / Hedgehog 'on' state / protein destabilization / mitotic spindle / Wnt signaling pathway / spindle pole / G1/S transition of mitotic cell cycle / Regulation of RAS by GAPs / protein polyubiquitination / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / Neddylation / gene expression / ubiquitin-dependent protein catabolic process / postsynapse / symbiont-mediated perturbation of host ubiquitin-like protein modification / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / Potential therapeutics for SARS / protein ubiquitination / inflammatory response / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of cell population proliferation / Golgi apparatus / negative regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Vaccinia virus WR Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Gao, G. / Graham, S.C. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Molecular basis of cullin-3 (Cul3) ubiquitin ligase subversion by vaccinia virus protein A55. Authors: Gao, C. / Pallett, M.A. / Croll, T.I. / Smith, G.L. / Graham, S.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i2m.cif.gz | 233.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i2m.ent.gz | 188.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i2m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i2m_validation.pdf.gz | 446.4 KB | Display | wwPDB validaton report |
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Full document | 6i2m_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 6i2m_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 6i2m_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/6i2m ftp://data.pdbj.org/pub/pdb/validation_reports/i2/6i2m | HTTPS FTP |
-Related structure data
Related structure data | 1r29S 4eozS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.17863/CAM.33381 / Data set type: diffraction image data / Metadata reference: 10.17863/CAM.33381/ |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29960.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal GSKH6 represent the cloning site and purification tag Source: (gene. exp.) Vaccinia virus WR / Gene: KBTB1, VACWR180, A55R / Plasmid: pOPTnH / Details (production host): C-terminal Lys-His6 tag / Production host: Escherichia coli (E. coli) / References: UniProt: P24768 |
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#2: Protein | Mass: 45723.953 Da / Num. of mol.: 1 / Mutation: I342R and L346D Source method: isolated from a genetically manipulated source Details: ENLYFQSHHHHHHDYKDDDDK sequence represents TEV protease site, His6 purification tag and FLAG epitope tag. I342R and L346D mutations stabilise the N-terminal domain as previously published (PMID 23349464). Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Plasmid: CUL3A-c013 Details (production host): pNIC-CTHF backbone vector with Kanamycin selectable marker. Production host: Escherichia coli (E. coli) / References: UniProt: Q13618 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.29% tacsimate pH 6.5, 9.92% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2017 / Details: toroidal mirrors |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99.23 Å / Num. obs: 44144 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 76.887 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.04 / Rrim(I) all: 0.146 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 12.6 % / Rmerge(I) obs: 17.224 / Mean I/σ(I) obs: 0.1 / Num. unique obs: 3279 / CC1/2: 0.302 / Rpim(I) all: 4.996 / Rrim(I) all: 17.953 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EOZ, 1R29 Resolution: 2.3→58.29 Å / Cross valid method: FREE R-VALUE Details: Structure was refined against data processed with an anisotropic/elliptical resolution cutoff. Overall ellipsoidal completeness is 92.9% overall and 86.4% in the highest resolution shell. ...Details: Structure was refined against data processed with an anisotropic/elliptical resolution cutoff. Overall ellipsoidal completeness is 92.9% overall and 86.4% in the highest resolution shell. Structure factors against which the model was refined and final map coefficients are deposited in addition to the un-truncated original observed intensities.
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Displacement parameters | Biso mean: 73.2 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→58.29 Å
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