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Yorodumi- PDB-2b5l: Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b5l | ||||||
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Title | Crystal Structure of DDB1 In Complex with Simian Virus 5 V Protein | ||||||
Components |
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Keywords | PROTEIN BINDING/VIRAL PROTEIN / DDB1 / SV5-V / beta propeller / propeller cluster / zinc finger / PROTEIN BINDING-VIRAL PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / WD40-repeat domain binding / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / cullin family protein binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / proteasomal protein catabolic process / positive regulation of viral genome replication / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / positive regulation of gluconeogenesis / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Wnt signaling pathway / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / protein-macromolecule adaptor activity / Neddylation / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / DNA repair / virus-mediated perturbation of host defense response / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / RNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Simian virus 5 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Li, T. / Chen, X. / Garbutt, K.C. / Zhou, P. / Zheng, N. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: Structure of DDB1 in complex with a paramyxovirus V protein: viral hijack of a propeller cluster in ubiquitin ligase. Authors: Li, T. / Chen, X. / Garbutt, K.C. / Zhou, P. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b5l.cif.gz | 469.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b5l.ent.gz | 383.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b5l_validation.pdf.gz | 488.4 KB | Display | wwPDB validaton report |
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Full document | 2b5l_full_validation.pdf.gz | 649.2 KB | Display | |
Data in XML | 2b5l_validation.xml.gz | 107.1 KB | Display | |
Data in CIF | 2b5l_validation.cif.gz | 141.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b5/2b5l ftp://data.pdbj.org/pub/pdb/validation_reports/b5/2b5l | HTTPS FTP |
-Related structure data
Related structure data | 2b5mSC 2b5nC 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: 127117.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 13435359, UniProt: Q16531*PLUS #2: Protein | Mass: 23965.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian virus 5 / Genus: Rubulavirus / Gene: P/V / Production host: Escherichia coli (E. coli) / References: UniProt: P11207 #3: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 20000, sodium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→47.8 Å / Num. all: 92110 / Num. obs: 92110 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B5M Resolution: 2.85→47.8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.85→47.8 Å
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