[English] 日本語
Yorodumi- PDB-4cgz: Crystal structure of the Bloom's syndrome helicase BLM in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cgz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Bloom's syndrome helicase BLM in complex with DNA | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication / cellular response to camptothecin ...regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication / cellular response to camptothecin / t-circle formation / G-quadruplex DNA unwinding / telomeric D-loop disassembly / Y-form DNA binding / negative regulation of cell division / four-way junction helicase activity / G-quadruplex DNA binding / DNA double-strand break processing / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / DNA 3'-5' helicase / replisome / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of cyclin-dependent protein serine/threonine kinase activity / nuclear chromosome / replication fork processing / DNA unwinding involved in DNA replication / mitotic G2 DNA damage checkpoint signaling / 3'-5' DNA helicase activity / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / isomerase activity / telomere maintenance / helicase activity / replication fork / molecular function activator activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / protein homooligomerization / PML body / Meiotic recombination / nuclear matrix / p53 binding / protein complex oligomerization / chromosome / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / DNA replication / Regulation of TP53 Activity through Phosphorylation / DNA repair / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Newman, J.A. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Crystal Structure of the Bloom'S Syndrome Helicase Indicates a Role for the Hrdc Domain in Conformational Changes. Authors: Newman, J.A. / Savitsky, P. / Allerston, C.K. / Bizard, A.H. / Ozer, O. / Sarlos, K. / Liu, Y. / Pardon, E. / Steyaert, J. / Hickson, I.D. / Gileadi, O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cgz.cif.gz | 159.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cgz.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 4cgz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cgz_validation.pdf.gz | 715.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4cgz_full_validation.pdf.gz | 727.3 KB | Display | |
Data in XML | 4cgz_validation.xml.gz | 25 KB | Display | |
Data in CIF | 4cgz_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/4cgz ftp://data.pdbj.org/pub/pdb/validation_reports/cg/4cgz | HTTPS FTP |
-Related structure data
Related structure data | 4cdgSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 75692.094 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE, RESIDUES 636-1298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54132, DNA helicase |
---|---|
#2: DNA chain | Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#3: DNA chain | Mass: 5099.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-ADP / |
Sequence details | FIRST 2 RESIDUES REMAIN FOLLOWING CLEAVAGE OF PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 80 % / Description: NONE |
---|---|
Crystal grow | Details: 21% PEG 4000, 0.1M HEPES PH 7.6, 5% 2-PROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→48.68 Å / Num. obs: 23593 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 146.81 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CDG Resolution: 3.2→48.646 Å / SU ML: 0.47 / σ(F): 0.22 / Phase error: 33.26 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 178 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→48.646 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|