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- PDB-3we2: Structure of BLM RQC domain bound to a phosphate ion -

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Basic information

Entry
Database: PDB / ID: 3we2
TitleStructure of BLM RQC domain bound to a phosphate 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 / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / forked DNA-dependent helicase activity / 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 / resolution of DNA recombination intermediates / forked DNA-dependent helicase activity / 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 / DNA double-strand break processing / Y-form DNA binding / negative regulation of cell division / DNA 3'-5' helicase / four-way junction helicase activity / G-quadruplex DNA binding / 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 / 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) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / helicase activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / protein homooligomerization / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / Meiotic recombination / nuclear matrix / p53 binding / single-stranded DNA binding / protein complex oligomerization / 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 / ATP hydrolysis activity / protein homodimerization 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding 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 / PHOSPHATE ION / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)32,7454
Polymers32,5912
Non-polymers1542
Water362
1
A: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4503
Polymers16,2961
Non-polymers1542
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)59.218, 59.218, 210.146
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-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8356.48
2
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

Diffraction
IDMean temperature (K)Crystal-ID
1901
2902
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9788, 0.9791, 0.9948
Detector
TypeIDDetectorDate
RAYONIX MX225HE1CCDOct 20, 2010
RAYONIX MX225HE2CCDOct 20, 2010
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97881
30.97911
40.99481
ReflectionResolution: 2.7→20 Å / Num. obs: 10768 / % possible obs: 98.2 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 4.2 / % possible all: 87.6

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Processing

Software
NameClassification
HKL-2000data collection
SHARPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.271 541 Random
Rwork0.237 --
obs-10768 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 9 2 1839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.413

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