[English] 日本語
![](img/lk-miru.gif)
- PDB-4cdg: Crystal structure of the Bloom's syndrome helicase BLM in complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4cdg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Bloom's syndrome helicase BLM in complex with Nanobody | ||||||
![]() |
| ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Savitsky, P. / Allerston, C.K. / Pike, A.C.W. / Pardon, E. / Steyaert, J. / Arrowsmith, C.H. / von Delft, F. / Bountra, C. / Edwards, A. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 305.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 242.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cgzC ![]() 2wwyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||
2 | ![]()
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.9999, 0.01281, -0.00243), Vector: |
-
Components
#1: Protein | Mass: 76705.219 Da / Num. of mol.: 2 / Fragment: CATALYTIC CORE, RESIDUES 636-1298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 16170.299 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: ISOLATED FROM PHAGE DISPLAY SCREENING OF CDNA OF IMMUNIZED LAMA Cell: B-LYMPHOCYTE / Production host: ![]() ![]() #3: Chemical | #4: Chemical | Sequence details | FIRST TWO RESIDUES ARE REMAINING FROM PURIFICATION TAG AFTER CLEAVAGE ISOLATED FROM IMMUNIZED LAMA, ...FIRST TWO RESIDUES ARE REMAINING FROM PURIFICATI | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.92 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1M MES PH 6.0, 22% PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→88 Å / Num. obs: 43258 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 67.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.2 / % possible all: 98.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WWY Resolution: 2.794→42.881 Å / SU ML: 0.4 / σ(F): 0.02 / Phase error: 30.17 / 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: 69.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.794→42.881 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|