[English] 日本語
Yorodumi- PDB-4e5z: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4e5z | ||||||
---|---|---|---|---|---|---|---|
Title | Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / BETA BARREL / PROTEIN-DNA COMPLEX / DOUBLE HELIX / damage / DNA repair / Host-virus interactions / Protein ubiquitination / Proteosomal degradation / DNA BINDING PROTEIN-DNA 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 / regulation of mitotic cell cycle phase transition / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity ...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 / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / viral release from host cell / pyrimidine dimer repair / ectopic germ cell programmed cell death / proteasomal protein catabolic process / protein autoubiquitination / positive regulation of viral genome replication / response to UV / positive regulation of gluconeogenesis / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Recognition of DNA damage by PCNA-containing replication complex / DNA Damage Recognition in GG-NER / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 / protein polyubiquitination / positive regulation of protein catabolic process / cellular response to UV / rhythmic process / cell junction / Neddylation / protein-macromolecule adaptor activity / site of double-strand break / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / chromosome, telomeric region / Ub-specific processing proteases / protein ubiquitination / DNA repair / DNA damage response / protein-containing complex binding / chromatin / nucleolus / negative regulation of apoptotic process / apoptotic process / protein-containing complex / DNA binding / extracellular space / extracellular exosome / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Yeh, J.I. / Du, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Authors: Yeh, J.I. / Levine, A.S. / Du, S. / Chinte, U. / Ghodke, H. / Wang, H. / Shi, H. / Hsieh, C.L. / Conway, J.F. / Van Houten, B. / Rapic-Otrin, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4e5z.cif.gz | 665.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4e5z.ent.gz | 539 KB | Display | PDB format |
PDBx/mmJSON format | 4e5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/4e5z ftp://data.pdbj.org/pub/pdb/validation_reports/e5/4e5z | HTTPS FTP |
---|
-Related structure data
Related structure data | 4e54C 3ei2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 128478.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, DDB1_HUMAN, Q16531, XAP1 Plasmid: pBlueBac4.5/V5-His NT-His10-DDB1pBlueBac4.5/V5-His NT-His10-DDB1 Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531 |
---|---|
#2: Protein | Mass: 49059.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDB2 / Plasmid: pBlueBac4.5/V5-HisNT-FLAG-DDB2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92466 |
#3: DNA chain | Mass: 7424.801 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic single stranded 24-oligodeoxynucleotides with complementary strand sequence: 5-TGACTGTATGATGACGATGCTGAC-3 |
#4: DNA chain | Mass: 7189.646 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthetic single stranded oligodeoxynucleotides with a central tetrahydrofuran abasic site mimic (3DR) on coding strand with sequence: 5-GTCAGCATCG(3DR)CATCATACAGTCA-3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.19 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24- ...Details: 20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: monochromators |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.2→41.093 Å / Num. all: 36260 / Num. obs: 33928 / % possible obs: 77.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 38.09 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.105 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.358 / % possible all: 77.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EI2 Resolution: 3.22→41.093 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU ML: 0.44 / σ(F): 0 / Phase error: 30.96 / Stereochemistry target values: MLHL Details: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF ...Details: THE MODEL WAS REFINED USING ITERATIVE CYCLES OF TLS AND RESTRAINED REFINEMENT (INCLUDING SECONDARY STRUCTURE, GEOMETRY, AND TORSION ANGLE RESTRAINTS) THROUGH PHENIX. CAREFUL INSPECTION OF WEIGHTED AND UNWEIGHTED MAPS, IN PARTICULAR, THE DIFFERENCE FOURIER MAPS, AFTER EACH REFINEMENT ROUND VERIFIED CORRECTNESS OF REGIONS MODIFIED OR EXTENDED IN THE PREVIOUS CYCLE. PROGRAMMATIC DIFFERENCES IN THE APPLICATION AND SCALING OF TLS PARAMETERS MAY RESULT IN VARIATIONS IN THE MAPS CALCULATED USING THE SF DIRECTLY DOWNLOADED FROM THE DATABASE. CALCULATING STRUCTURE FACTORS (SF) USING MODEL COORDINATES AND THERMAL PARAMETERS FROM THE DEPOSITED PDB FILES IN PHENIX WILL REPRODUCE THE MAPS AND CONFORMATIONAL FEATURES DESCRIBED BY THE AUTHORS IN THE CITATION.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 185.363 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.22→41.093 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|