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Yorodumi- PDB-3i7p: Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i7p | ||||||
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Title | Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A | ||||||
Components |
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Keywords | PROTEIN BINDING / DDB1 / WDR40A / DCAF12 / H-Box Motif / Cytoplasm / DNA damage / DNA repair / DNA-binding / Host-virus interaction / Nucleus / Phosphoprotein / Polymorphism / Ubl conjugation / Ubl conjugation pathway / WD repeat | ||||||
Function / homology | Function and homology information positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / 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 / ubiquitin-like ligase-substrate adaptor activity / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of gluconeogenesis / T cell activation / regulation of autophagy / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / regulation of circadian rhythm / 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 / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / protein ubiquitination / DNA repair / centrosome / apoptotic process / DNA damage response / protein-containing complex binding / nucleolus / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Li, T. / Robert, E.I. / Breugel, P.C.V. / Strubin, M. / Zheng, N. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: A promiscuous alpha-helical motif anchors viral hijackers and substrate receptors to the CUL4-DDB1 ubiquitin ligase machinery. Authors: Li, T. / Robert, E.I. / van Breugel, P.C. / Strubin, M. / Zheng, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i7p.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i7p.ent.gz | 170.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7p ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7p | HTTPS FTP |
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-Related structure data
Related structure data | 3i7hC 3i7kC 3i7lC 3i7nC 3i7oC 3i89C 3i8cC 3i8eC 2b5mS 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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Unit cell |
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-Components
#1: Protein | Mass: 127399.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 |
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#2: Protein/peptide | Mass: 1655.960 Da / Num. of mol.: 1 / Fragment: Residues 45-57 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5T6F0 |
Sequence details | MUTATIONS OCCURRED DURING THE CLONING OF DDB1 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 173 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0,1.005 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 28, 2008 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3→45.79 Å / Num. all: 29177 / Num. obs: 26351 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 27.7 | |||||||||
Reflection shell | Resolution: 3→3.078 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.4 / % possible all: 89.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2B5M Resolution: 3→45.79 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.86 / SU B: 21.551 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.557 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 80.631 Å2
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Refinement step | Cycle: LAST / Resolution: 3→45.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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