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- PDB-4cgz: Crystal structure of the Bloom's syndrome helicase BLM in complex... -
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Basic information
Entry | Database: PDB / ID: 4cgz | ||||||
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Title | Crystal structure of the Bloom's syndrome helicase BLM in complex with DNA | ||||||
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![]() | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 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 / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 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 / G-quadruplex DNA unwinding / t-circle formation / telomeric D-loop disassembly / Y-form DNA binding / negative regulation of cell division / four-way junction helicase activity / G-quadruplex DNA binding / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / DNA double-strand break processing / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / DNA 3'-5' helicase / 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 / 3'-5' DNA helicase activity / nuclear chromosome / regulation of cyclin-dependent protein serine/threonine kinase activity / DNA unwinding involved in DNA replication / replication fork processing / mitotic G2 DNA damage checkpoint signaling / 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 / telomere maintenance / isomerase activity / replication fork / helicase activity / molecular function activator activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / protein homooligomerization / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.3 KB | Display | ![]() |
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PDB format | ![]() | 119.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cdgSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() |
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#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 80 % / Description: NONE |
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Crystal grow | Details: 21% PEG 4000, 0.1M HEPES PH 7.6, 5% 2-PROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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: 178 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→48.646 Å
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Refine LS restraints |
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LS refinement shell |
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