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- PDB-4o3m: Ternary complex of Bloom's syndrome helicase -

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Basic information

Entry
Database: PDB / ID: 4o3m
TitleTernary complex of Bloom's syndrome helicase
Components
  • 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'
  • Bloom syndrome protein
KeywordsHydrolase/DNA / Winged Helix / Helicase / 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 / ATP-dependent activity, acting on DNA / response to X-ray / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSwan, M.K. / Bertrand, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA.
Authors: Swan, M.K. / Legris, V. / Tanner, A. / Reaper, P.M. / Vial, S. / Bordas, R. / Pollard, J.R. / Charlton, P.A. / Golec, J.M. / Bertrand, J.A.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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 syndrome protein
P: 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'
T: 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,21114
Polymers87,1823
Non-polymers1,02911
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-25 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.930, 164.680, 50.980
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 75002.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 BL21(DE3) / References: UniProt: P54132, DNA helicase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'


Mass: 4932.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised oligonucleotide.
#3: DNA chain 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'


Mass: 7247.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised oligonucleotide.

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Non-polymers , 5 types, 71 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: 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
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6-10% Isopropanol, 50mM MES, 10mM magnesium chloride., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013 / Details: slits
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→35.91 Å / Num. all: 36392 / Num. obs: 36392 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 59.56 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.025 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2666 / Rsym value: 0.498 / % possible all: 99

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Processing

Software
NameVersionClassification
SHARPphasing
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 2V1X

2v1x


Resolution: 2.3→35.91 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9204 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1735 5.01 %RANDOM
Rwork0.1811 ---
all0.1829 34639 --
obs0.1829 34639 94.05 %-
Displacement parametersBiso mean: 85.6 Å2
Baniso -1Baniso -2Baniso -3
1--33.2893 Å20 Å21.9695 Å2
2--18.9673 Å20 Å2
3---14.322 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 570 61 60 5412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015518HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077580HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1816SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes754HARMONIC5
X-RAY DIFFRACTIONt_it5518HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion20.71
X-RAY DIFFRACTIONt_chiral_improper_torsion739SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6064SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2336 125 5.03 %
Rwork0.2141 2359 -
all0.2152 2484 -
obs--94.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0331-0.74320.15182.8195-0.4142.3938-0.09170.10440.1319-0.02210.00650.108-0.0150.07860.0852-0.2556-0.005-0.016-0.42590.0365-0.4082119.341923.505658.2881
21.80850.3909-1.01984.06470.13133.30210.1337-0.1556-0.17160.4443-0.14150.15630.14830.00020.0077-0.1410.05660.0384-0.39880.0117-0.4355120.9827-6.458668.6107
32.1456-0.4618-0.29318.6766-0.14474.0707-0.14050.6618-0.1671-0.40550.25110.72540.0237-0.678-0.1106-0.03720.06270.0037-0.1939-0.0425-0.2463117.4028-14.932449.7463
44.957-0.1307-1.26421.09120.53845.8626-0.2123-0.12010.4048-0.27870.136-1.5439-0.53011.17310.07630.13470.03010.0541-0.1498-0.06610.2303137.7842-4.437454.9265
54.2479-1.23590.085512.48541.58422.3610.14970.1896-0.1248-0.95590.0424-0.4354-0.301-0.2027-0.1921-0.06570.04030.0437-0.4033-0.0079-0.3637125.022-30.155143.9357
64.2526-0.1353-0.01411.9166-0.44925.7201-0.1158-0.3230.14660.2955-0.1074-0.2241-0.0960.88810.2233-0.11110.0675-0.0548-0.17310.019-0.443132.155913.213284.1131
77.06794.4478-3.62320-7.08463.9954-0.1325-0.2099-0.91140.4028-0.18510.84910.5223-0.8370.31760.078-0.22810.3664-0.59130.0155-0.1288112.1717-36.45257.5364
84.66212.69751.75162.0649-4.20250.0085-0.0966-0.26510.15940.42010.2496-0.04380.15030.2706-0.1530.42760.2701-0.0921-0.54490.1281-0.4982124.2676-34.24167.4404
93.3217-1.6252-3.53990.6015-5.487-0.0173-0.08020.187-0.47260.18560.0894-0.32780.31190.2796-0.00920.41520.547-0.2411-0.02440.32880.467136.0595-42.79367.4843
101.10921.75582.26193.8532-1.48133.06510.01-0.30560.29330.0030.0824-0.0005-0.34780.1342-0.09240.38790.0273-0.61370.03030.2580.1677138.7558-33.839265.3098
111.901-0.9888-1.88925.0542-2.397214.3362-0.0251-0.3886-0.51261.3072-0.06361.02250.317-0.54620.08870.06080.11210.0996-0.47440.1031-0.2864123.2701-40.44963.9568
123.260.2942-5.262110.033511.2206-0.0257-0.1426-0.385-0.084-0.1205-0.33610.59210.5631-0.48470.4786-0.2931-0.022-0.0288-0.4906-0.0324-0.4623108.7164-20.713461.7505
130.0788-1.25730.40630.21720.23360.4764-0.03340.05630.026-0.01380.0390.03510.0045-0.0208-0.00560.58830.2647-0.07120.0923-0.09430.1359104.1594-1.436958.0734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|636 - 856 }A636 - 856
2X-RAY DIFFRACTION2{ A|857 - 993 }A857 - 993
3X-RAY DIFFRACTION3{ A|994 - 1032 }A994 - 1032
4X-RAY DIFFRACTION4{ A|1033 - 1068 }A1033 - 1068
5X-RAY DIFFRACTION5{ A|1069 - 1195 }A1069 - 1195
6X-RAY DIFFRACTION6{ A|1205 - 1298 }A1205 - 1298
7X-RAY DIFFRACTION7{ P|1 - 5 }P1 - 5
8X-RAY DIFFRACTION8{ P|6 - 9 }P6 - 9
9X-RAY DIFFRACTION9{ P|10 - 16 }P10 - 16
10X-RAY DIFFRACTION10{ T|1 - 6 }T1 - 6
11X-RAY DIFFRACTION11{ T|7 - 12 }T7 - 12
12X-RAY DIFFRACTION12{ T|13 - 18 }T13 - 18
13X-RAY DIFFRACTION13{ T|19 - 24 }T19 - 24

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