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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
TitleCrystal structure of the Bloom's syndrome helicase BLM in complex with DNA
Components
  • 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP)-3'
  • 5'-D(*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*DT *CP*CP*CP)-3'
  • BLOOM'S SYNDROME HELICASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / 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 / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin ...RecQ family helicase-topoisomerase III complex / 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 / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin / DNA geometric change / Y-form DNA binding / negative regulation of cell division / cellular response to hydroxyurea / G-quadruplex DNA binding / lateral element / negative regulation of DNA recombination / bubble DNA binding / DNA double-strand break processing / Impaired BRCA2 binding to PALB2 / Processive synthesis on the C-strand of the telomere / regulation of cyclin-dependent protein serine/threonine kinase activity / 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) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / replication fork processing / 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 / DNA helicase activity / four-way junction DNA binding / telomere maintenance / replication fork / cellular response to ionizing radiation / isomerase activity / helicase activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / protein homooligomerization / Meiotic recombination / HDR through Homologous Recombination (HRR) / nuclear matrix / p53 binding / single-stranded DNA binding / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / DNA repair / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / 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 / HRDC domain / RQC domain / RQC / RQC 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 / HRDC domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 / DNA polymerase; domain 1 / 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 / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsNewman, J.A. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
CitationJournal: Nucleic Acids Res. / Year: 2015
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
DepositionNov 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: BLOOM'S SYNDROME HELICASE
B: 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP)-3'
C: 5'-D(*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*DT *CP*CP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9715
Polymers84,4793
Non-polymers4932
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-27.4 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.530, 149.530, 64.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42

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Components

#1: Protein BLOOM'S SYNDROME HELICASE / DNA HELICASE / RECQ-LIKE TYPE 2 / RECQ2 / RECQ PROTEIN-LIKE 3


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.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54132, DNA helicase
#2: DNA chain 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP)-3'


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*DT *CP*CP*CP)-3'


Mass: 5099.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Sequence detailsFIRST 2 RESIDUES REMAIN FOLLOWING CLEAVAGE OF PURIFICATION TAG

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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: 4.19 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growDetails: 21% PEG 4000, 0.1M HEPES PH 7.6, 5% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CDG

4cdg


Resolution: 3.2→48.646 Å / SU ML: 0.47 / σ(F): 0.22 / Phase error: 33.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 2272 5 %
Rwork0.2291 --
obs0.2305 23555 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 178 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 582 28 0 5591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065757
X-RAY DIFFRACTIONf_angle_d1.1337898
X-RAY DIFFRACTIONf_dihedral_angle_d18.2232183
X-RAY DIFFRACTIONf_chiral_restr0.048889
X-RAY DIFFRACTIONf_plane_restr0.005907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.26960.42591500.37822639X-RAY DIFFRACTION100
3.2696-3.34570.36011720.36622704X-RAY DIFFRACTION100
3.3457-3.42930.39551630.36972654X-RAY DIFFRACTION99
3.4293-3.5220.33061350.34382740X-RAY DIFFRACTION100
3.522-3.62560.37851370.32242709X-RAY DIFFRACTION100
3.6256-3.74260.36741310.32752718X-RAY DIFFRACTION99
3.7426-3.87630.3381430.30592695X-RAY DIFFRACTION100
3.8763-4.03140.2941040.27442734X-RAY DIFFRACTION100
4.0314-4.21480.28111410.26542716X-RAY DIFFRACTION100
4.2148-4.43690.2651590.23082684X-RAY DIFFRACTION100
4.4369-4.71460.20611750.21332663X-RAY DIFFRACTION100
4.7146-5.07830.21591330.20682731X-RAY DIFFRACTION100
5.0783-5.58870.1981410.21132712X-RAY DIFFRACTION99
5.5887-6.39590.23691210.23212718X-RAY DIFFRACTION99
6.3959-8.05220.30481300.24262707X-RAY DIFFRACTION99
8.0522-48.65140.23571370.18542657X-RAY DIFFRACTION98

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