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Yorodumi- PDB-7ukn: Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ukn | |||||||||||||||||||||
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Title | Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 | |||||||||||||||||||||
Components |
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Keywords | PROTEIN BINDING / DDB1 / pUL145 / HCMV / Human Cytomegalovirus / H-box / E3 ligase | |||||||||||||||||||||
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 / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / positive regulation of gluconeogenesis / proteasomal protein catabolic process / 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 / rhythmic process / cellular response to UV / protein-macromolecule adaptor activity / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / damaged DNA binding / protein ubiquitination / DNA repair / 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 / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) Human betaherpesvirus 5 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||||||||||||||
Authors | Wick, E.T. / Treadway, C.J. / Nicely, N.I. / Li, Z. / Ren, Z. / Baldwin, A.S. / Xiong, Y. / Harrison, J.S. / Brown, N.G. | |||||||||||||||||||||
Funding support | United States, 6items
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Citation | Journal: J.Virol. / Year: 2022 Title: Insight into Viral Hijacking of CRL4 Ubiquitin Ligase through Structural Analysis of the pUL145-DDB1 Complex. Authors: Wick, E.T. / Treadway, C.J. / Li, Z. / Nicely, N.I. / Ren, Z. / Baldwin, A.S. / Xiong, Y. / Harrison, J.S. / Brown, N.G. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ukn.cif.gz | 524.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ukn.ent.gz | 356.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ukn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uk/7ukn ftp://data.pdbj.org/pub/pdb/validation_reports/uk/7ukn | HTTPS FTP |
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-Related structure data
Related structure data | 3i7lS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 127225.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16531 |
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#2: Protein/peptide | Mass: 1418.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Residues 25-37 of Protein UL145 / Source: (synth.) Human betaherpesvirus 5 / References: UniProt: F5HF44 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100 mM MES (pH 6.5-6.7), 16% PEG 4000, 50 mM NaCl, 5 mM DTT PH range: 6.5-6.7 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→46.21 Å / Num. obs: 34718 / % possible obs: 97.37 % / Redundancy: 6.3 % / Biso Wilson estimate: 50.78 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.07 / Rrim(I) all: 0.18 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.87→2.92 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.793 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2877 / CC1/2: 0.488 / CC star: 0.81 / Rpim(I) all: 0.84 / % possible all: 82.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I7L Resolution: 2.9→46.21 Å / SU ML: 0.4125 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.026 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 58.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.21 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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