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- PDB-9i0s: Structure of RecQL-ADP complex from Bos taurus -

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Basic information

Entry
Database: PDB / ID: 9i0s
TitleStructure of RecQL-ADP complex from Bos taurus
ComponentsATP-dependent DNA helicase
KeywordsHYDROLASE / helicase DNA G-quadruplex
Function / homology
Function and homology information


four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / double-strand break repair via homologous recombination / chromosome / nucleic acid binding / DNA replication / hydrolase activity / ATP binding / metal ion binding ...four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / double-strand break repair via homologous recombination / chromosome / nucleic acid binding / DNA replication / hydrolase activity / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 ...ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / ATP-dependent DNA helicase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSong, Z.Y. / Liu, N.N. / Ai, X. / Rety, S. / Xi, X.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32301042, 32071291, 32071225 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural mechanism of RECQ1 helicase in unfolding G-quadruplexes compared with duplex DNA.
Authors: Song, Z.Y. / Zhang, X. / Ai, X. / Huang, L.Y. / Hou, X.M. / Fosse, P. / Liu, N.N. / Mauffret, O. / Rety, S. / Xi, X.G.
History
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2399
Polymers121,1112
Non-polymers1,1297
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-53 kcal/mol
Surface area45890 Å2
Unit cell
Length a, b, c (Å)55.153, 119.450, 201.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 63 through 69 or resid 71...
d_2ens_1(chain "B" and (resid 63 through 69 or resid 71...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERASNASNAA63 - 692 - 8
d_12GLUGLUVALVALAA71 - 7910 - 18
d_13ASPASPLYSLYSAA81 - 15220 - 91
d_14LEULEUASNASNAA154 - 17993 - 118
d_15ASNASNSERSERAA181 - 182120 - 121
d_16LEULEULYSLYSAA184 - 198123 - 137
d_17PHEPHEGLUGLUAA200 - 205139 - 144
d_18ALAALASERSERAA207 - 259146 - 198
d_19VALVALGLNGLNAA261 - 266200 - 205
d_110ILEILEVALVALAA268 - 271207 - 210
d_111CYSCYSSERSERAA274 - 280213 - 219
d_112ASNASNILEILEAA282 - 301221 - 240
d_113ASPASPVALVALAA303 - 305242 - 244
d_114LEULEUTYRTYRAA307 - 312246 - 251
d_115GLYGLYSERSERAA314 - 323253 - 262
d_116LYSLYSTHRTHRAA325 - 354264 - 293
d_117VALVALMETMETAA356 - 410295 - 349
d_118ALAALAGLNGLNAA412 - 437351 - 376
d_119LYSLYSALAALAAA439 - 459378 - 398
d_120PHEPHEASPASPAA462 - 463401 - 402
d_121ALAALAASNASNAA470 - 472409 - 411
d_122METMETCYSCYSAA474 - 479413 - 418
d_123ILEILEGLUGLUAA482 - 485421 - 424
d_124LYSLYSCYSCYSAA487 - 493426 - 432
d_125ASPASPILEILEAA495 - 497434 - 436
d_126ILEILEGLUGLUAA499 - 508438 - 447
d_127LEULEUSERSERAA510 - 525449 - 464
d_128GLYGLYLYSLYSAA531 - 591470 - 530
d_129ZNZNZNZNAC1001
d_130ADPADPADPADPAD1002
d_21SERSERASNASNBB63 - 692 - 8
d_22GLUGLUVALVALBB71 - 7910 - 18
d_23ASPASPLYSLYSBB81 - 15220 - 91
d_24LEULEUASNASNBB154 - 17993 - 118
d_25ASNASNSERSERBB181 - 182120 - 121
d_26LEULEULYSLYSBB184 - 198123 - 137
d_27PHEPHEGLUGLUBB200 - 205139 - 144
d_28ALAALASERSERBB207 - 259146 - 198
d_29VALVALGLNGLNBB261 - 266200 - 205
d_210ILEILEVALVALBB268 - 271207 - 210
d_211CYSCYSSERSERBB274 - 280213 - 219
d_212ASNASNILEILEBB282 - 301221 - 240
d_213ASPASPVALVALBB303 - 305242 - 244
d_214LEULEUTYRTYRBB307 - 312246 - 251
d_215GLYGLYSERSERBB314 - 323253 - 262
d_216LYSLYSTHRTHRBB325 - 354264 - 293
d_217VALVALMETMETBB356 - 410295 - 349
d_218ALAALAGLNGLNBB412 - 437351 - 376
d_219LYSLYSALAALABB439 - 459378 - 398
d_220PHEPHEASPASPBB462 - 463401 - 402
d_221ALAALAASNASNBB470 - 472409 - 411
d_222METMETCYSCYSBB474 - 479413 - 418
d_223ILEILEGLUGLUBB482 - 485421 - 424
d_224LYSLYSCYSCYSBB487 - 493426 - 432
d_225ASPASPILEILEBB495 - 497434 - 436
d_226ILEILEGLUGLUBB499 - 508438 - 447
d_227LEULEUSERSERBB510 - 525449 - 464
d_228GLYGLYLYSLYSBB531 - 591470 - 530
d_229ZNZNZNZNBG1001
d_230ADPADPADPADPBH1002

NCS oper: (Code: givenMatrix: (0.469973926256, 0.310148557831, -0.826397229373), (0.311159505098, -0.934347970084, -0.173705593422), (-0.826017113035, -0.175504253153, -0.535624855752)Vector: 12. ...NCS oper: (Code: given
Matrix: (0.469973926256, 0.310148557831, -0.826397229373), (0.311159505098, -0.934347970084, -0.173705593422), (-0.826017113035, -0.175504253153, -0.535624855752)
Vector: 12.5111590944, 1.63350640147, 24.0159762567)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-dependent DNA helicase


Mass: 60555.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RECQL / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K-12 / References: UniProt: A0JN36, DNA helicase

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: Tris-HCl 20mM KCl 100mM DTT 1mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→50.48 Å / Num. obs: 47036 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 58.79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.214 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 11.5 % / Rmerge(I) obs: 3.118 / Mean I/σ(I) obs: 1 / Num. unique obs: 2275 / CC1/2: 0.416 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50.48 Å / SU ML: 0.3479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.7911
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 2271 4.83 %
Rwork0.2398 44740 -
obs0.2412 47011 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.29 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8466 0 63 62 8591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348708
X-RAY DIFFRACTIONf_angle_d0.769611754
X-RAY DIFFRACTIONf_chiral_restr0.04961296
X-RAY DIFFRACTIONf_plane_restr0.0051480
X-RAY DIFFRACTIONf_dihedral_angle_d17.82053303
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.14801528686 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.32721280.33412730X-RAY DIFFRACTION100
2.56-2.620.35291350.33122780X-RAY DIFFRACTION99.97
2.62-2.680.38621370.32182715X-RAY DIFFRACTION99.96
2.68-2.750.36261330.31342820X-RAY DIFFRACTION99.97
2.75-2.830.32251170.32532746X-RAY DIFFRACTION100
2.83-2.930.4061550.34882758X-RAY DIFFRACTION100
2.93-3.030.40091300.33372773X-RAY DIFFRACTION100
3.03-3.150.31651590.30192750X-RAY DIFFRACTION100
3.15-3.30.34741450.28562775X-RAY DIFFRACTION99.93
3.3-3.470.29931520.27012778X-RAY DIFFRACTION100
3.47-3.690.28551370.25952807X-RAY DIFFRACTION100
3.69-3.970.27841480.2292810X-RAY DIFFRACTION100
3.97-4.370.22081310.2032792X-RAY DIFFRACTION100
4.37-50.22341480.18992855X-RAY DIFFRACTION100
5-6.30.22511330.21352869X-RAY DIFFRACTION99.97
6.3-50.480.19961830.17962982X-RAY DIFFRACTION99.56
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)
11.52649523058-0.244057729722-0.2837759566353.75055229041-2.535874171086.709403083050.06496755109250.0954710466140.0866320653474-0.0690838548636-0.168095667333-0.0517033543195-0.8122049533030.02991521140510.08765400136890.7258731830620.000345651038783-0.05369871868750.444575140592-0.04024603481360.33366808336-23.4359596105-20.491593318511.1230640129
21.189405780940.1155721576890.2440977508181.720466459060.4768979504913.536614153480.01995322253840.2130340974820.0720253985329-0.248796646062-0.00569021186625-0.2701754561780.1827410700320.411275234903-0.04183040714880.3531043992560.08146483258870.0699337827940.3928072185070.05792180791530.410013889286-7.6901542966-27.408423989643.1896128959
32.61293633531-2.28802068748-0.01459888002522.82640698255-0.4880811570940.9730126002780.05337812054430.01996159045290.152477657736-0.0984770201296-0.116828561313-0.2720869957820.01796607783810.0378026322905-0.1232326506590.332921329721-0.0779289830010.02965235489590.3865154313590.005998964121050.484792237688-14.195280705911.445458416341.0643106882
41.63867103129-0.357174571760.4813292848854.08558706059-0.1434772446213.004035531220.3646131289760.4028291761040.0310647665317-1.3675941662-0.266532028028-0.2010304128940.4169508458160.108277430038-0.2380429552740.9187612888840.1348587760210.1016422424240.4756110169280.09149691519020.413613456672-35.296643854317.484862044511.9493657476
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 62 through 285 )AA62 - 2851 - 224
22chain 'A' and (resid 286 through 592 )AA286 - 592225 - 531
33chain 'B' and (resid 63 through 285 )BE63 - 2851 - 223
44chain 'B' and (resid 286 through 592 )BE286 - 592224 - 530

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