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- PDB-3we3: Structure of BLM RQC domain bound to an arsenate ion -

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Basic information

Entry
Database: PDB / ID: 3we3
TitleStructure of BLM RQC domain bound to an arsenate ion
ComponentsBloom syndrome protein
KeywordsDNA BINDING PROTEIN / Winged-Helix / DNA helicase / DNA binding
Function / homology
Function and homology information


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 / telomeric D-loop binding / DNA/DNA annealing activity / 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 / telomeric D-loop binding / DNA/DNA annealing activity / 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 / DNA double-strand break processing / 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 / Homologous DNA Pairing and Strand Exchange / 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 / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / nuclear chromosome / DNA unwinding involved in DNA replication / protein complex oligomerization / 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 / replication fork / molecular function activator activity / isomerase activity / cellular response to ionizing radiation / helicase activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / protein homooligomerization / HDR through Homologous Recombination (HRR) / PML body / Meiotic recombination / nuclear matrix / p53 binding / single-stranded DNA binding / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / 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
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / ARSENATE / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, S.Y. / Hakoshima, T. / Kitano, K.
CitationJournal: Sci Rep / Year: 2013
Title: Structure of the RecQ C-terminal Domain of Human Bloom Syndrome Protein
Authors: Kim, S.Y. / Hakoshima, T. / Kitano, K.
History
DepositionJun 28, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references / Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bloom syndrome protein
B: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7894
Polymers32,5912
Non-polymers1982
Water362
1
A: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4943
Polymers16,2961
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bloom syndrome protein


Theoretical massNumber of molelcules
Total (without water)16,2961
Polymers16,2961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.717, 59.717, 209.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Bloom syndrome protein / BLM / DNA helicase / RecQ-like type 2 / RecQ2 / RecQ protein-like 3


Mass: 16295.717 Da / Num. of mol.: 2
Fragment: RecQ C-terminal (RQC) domain, UNP residues 1068-1209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM / Plasmid: pGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus RIL / References: UniProt: P54132, DNA helicase
#2: Chemical ChemComp-ART / ARSENATE


Mass: 138.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AsO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.4
Details: 20-25% PEG 4000, 50mM sodium phosphate, 150mM sodium acetate, 100mM Tris-HCl, 15%(v/v) glycerol, pH 8.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 8985 / % possible obs: 99 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 5 / % possible all: 93.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WE2

3we2


Resolution: 2.9→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 425 Random
Rwork0.269 --
obs-8985 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 9 2 1828
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg1.312

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