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Basic information

Entry
Database: PDB / ID: 7auc
TitleCrystal structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)
ComponentsBloom syndrome protein,Bloom syndrome protein
KeywordsNUCLEAR PROTEIN / Helicase / RecQ / BLM / DNA Repair
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 / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsChen, X. / Oliver, A.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC302/A24386 United Kingdom
Wellcome Trust110578/Z/15/Z United Kingdom
Citation
Journal: Elife / Year: 2021
Title: Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein.
Authors: Chen, X. / Ali, Y.I. / Fisher, C.E. / Arribas-Bosacoma, R. / Rajasekaran, M.B. / Williams, G. / Walker, S. / Booth, J.R. / Hudson, J.J. / Roe, S.M. / Pearl, L.H. / Ward, S.E. / Pearl, F.M. / Oliver, A.W.
#1: Journal: Biorxiv / Year: 2020
Title: Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Authors: Chen, X. / Ali, Y. / Fisher, C.E.L. / Arribas-Bosacoma, R. / Rajasekaran, M.B. / Williams, G. / Walker, S. / Roe, S.M. / Pearl, L.H. / Ward, S.E. / Pearl, F.M.G. / Oliver, A.W.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,59520
Polymers63,8841
Non-polymers1,71119
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-26 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.28, 107.69, 55.2
Angle α, β, γ (deg.)90, 109.31, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 63884.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54132, DNA helicase

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Non-polymers , 9 types, 450 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus-HT, condition A8, Molecular Dimensions 0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4 Divalents = 0.3M magnesium chloride, 0.3M calcium chloride Buffer system 2 ...Details: Morpheus-HT, condition A8, Molecular Dimensions 0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4 Divalents = 0.3M magnesium chloride, 0.3M calcium chloride Buffer system 2 = 1M sodium HEPES, MOPS (acid) pH 7.5 75% Precipitant Mix 4 = 25% w/v MPD, 25% v/v PEG1000, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.53→51.23 Å / Num. obs: 88499 / % possible obs: 98.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.58 Å2 / CC1/2: 1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.53→1.56 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8096 / CC1/2: 0.61 / % possible all: 90.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3M

4o3m


Resolution: 1.53→51.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4388 -RANDOM
Rwork0.1891 ---
obs0.1901 88464 98.3 %-
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.2284 Å20 Å25.847 Å2
2--6.3269 Å20 Å2
3----8.5553 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.53→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 95 431 4343
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084026HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.95444HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1871SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes688HARMONIC5
X-RAY DIFFRACTIONt_it4026HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3933SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion2.37
LS refinement shellResolution: 1.53→1.54 Å
RfactorNum. reflection% reflection
Rfree0.2186 91 -
Rwork0.2325 --
obs0.2318 1770 83.88 %

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