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Yorodumi- PDB-4a08: Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at... -
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-Basic information
Entry | Database: PDB / ID: 4a08 | ||||||
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Title | Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1) | ||||||
Components |
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Keywords | DNA-BINDING PROTEIN/DNA / DNA-BINDING PROTEIN-DNA COMPLEX / DNA DAMAGE REPAIR | ||||||
Function / homology | Function and homology information DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / 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 ...DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Neddylation / Ub-specific processing proteases / 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 / 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 / site of DNA damage / cullin family protein binding / viral release from host cell / ectopic germ cell programmed cell death / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / 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 / 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) DANIO RERIO (zebrafish) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation Authors: Scrima, A. / Fischer, E.S. / Iwai, S. / Gut, H. / Thoma, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a08.cif.gz | 310.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a08.ent.gz | 238.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/4a08 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/4a08 | HTTPS FTP |
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-Related structure data
Related structure data | 4a09C 4a0aC 4a0bC 4a0cC 4a0kC 4a0lC 4a11C 3ei1S C: citing same article (ref.) S: Starting model for refinement |
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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
-DNA DAMAGE-BINDING PROTEIN ... , 2 types, 2 molecules AB
#1: Protein | Mass: 129336.867 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC-DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q16531 |
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#2: Protein | Mass: 43418.102 Da / Num. of mol.: 1 / Fragment: RESIDUES 60-423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DANIO RERIO (zebrafish) / Plasmid: PFASTBAC-DERIVED / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q2YDS1 |
-DNA chain , 2 types, 2 molecules GH
#3: DNA chain | Mass: 4241.756 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: DAMAGED STRAND (CONTAINS CYCLOBUTANE PYRIMIDINE DIMER (TTD)) Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 4273.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: UNDAMAGED STRAND / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 20 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDNonpolymer details | CYCLOBUTAN | |
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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: 2.84 Å3/Da / Density % sol: 56.78 % / Description: NONE |
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Crystal grow | pH: 5.6 / Details: 100 MM MES, 25 MM NAOH, 18% PEG 350MME., pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 37332 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EI1 Resolution: 3→48.62 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.841 / SU B: 21.52 / SU ML: 0.401 / Cross valid method: THROUGHOUT / ESU R Free: 0.52 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.672 Å2
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Refinement step | Cycle: LAST / Resolution: 3→48.62 Å
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