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- PDB-9i23: Structure of Human helicase RecQ1- 795-2T G-quadruplex - ADP complex -

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Basic information

Entry
Database: PDB / ID: 9i23
TitleStructure of Human helicase RecQ1- 795-2T G-quadruplex - ADP complex
Components
  • ATP-dependent DNA helicase Q1
  • DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
KeywordsHYDROLASE / helicase DNA G-quadruplex
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / DNA helicase activity / double-strand break repair via homologous recombination / chromosome / DNA replication ...double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / replication fork processing / DNA helicase activity / double-strand break repair via homologous recombination / chromosome / DNA replication / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / metal ion binding / nucleus / membrane / 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 / : / DNA / DNA (> 10) / ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 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 17, 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 Q1
B: ATP-dependent DNA helicase Q1
C: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,54714
Polymers135,3574
Non-polymers1,19010
Water00
1
A: ATP-dependent DNA helicase Q1
C: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2737
Polymers67,6782
Non-polymers5955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent DNA helicase Q1
D: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2737
Polymers67,6782
Non-polymers5955
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.659, 155.659, 129.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 62 through 166 or resid 168...
d_2ens_1(chain "B" and (resid 62 through 166 or resid 168...

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_11ASPASPSERSERAA62 - 1661 - 105
d_12GLUGLUASNASNAA168 - 179107 - 118
d_13ASNASNSERSERAA181 - 225120 - 164
d_14TRPTRPSERSERAA227 - 280166 - 219
d_15ASNASNTHRTHRAA282 - 297221 - 236
d_16ASPASPTYRTYRAA299 - 312238 - 251
d_17GLYGLYGLNGLNAA314 - 324253 - 263
d_18ASPASPPROPROAA326 - 350265 - 289
d_19ASPASPLYSLYSAA352 - 359291 - 298
d_110SERSERALAALAAA361 - 373300 - 312
d_111GLYGLYTYRTYRAA377 - 399316 - 338
d_112GLUGLUGLNGLNAA401 - 438340 - 377
d_113LEULEUSERSERAA440 - 451379 - 390
d_114CYSCYSGLNGLNAA453 - 460392 - 399
d_115PHEPHEVALVALAA462 - 465401 - 404
d_116SERSERLYSLYSAA468 - 480407 - 419
d_117ALAALAALAALAAA483 - 525422 - 464
d_118LEULEULEULEUAA527466
d_119VALVALLYSLYSAA529 - 592468 - 531
d_120ZNZNZNZNAE1001
d_121ADPADPADPADPAF1002
d_21ASPASPSERSERBB62 - 1661 - 105
d_22GLUGLUASNASNBB168 - 179107 - 118
d_23ASNASNSERSERBB181 - 225120 - 164
d_24TRPTRPSERSERBB227 - 280166 - 219
d_25ASNASNTHRTHRBB282 - 297221 - 236
d_26ASPASPTYRTYRBB299 - 312238 - 251
d_27GLYGLYGLNGLNBB314 - 324253 - 263
d_28ASPASPPROPROBB326 - 350265 - 289
d_29ASPASPLYSLYSBB352 - 359291 - 298
d_210SERSERALAALABB361 - 373300 - 312
d_211GLYGLYTYRTYRBB377 - 399316 - 338
d_212GLUGLUGLNGLNBB401 - 438340 - 377
d_213LEULEUSERSERBB440 - 451379 - 390
d_214CYSCYSGLNGLNBB453 - 460392 - 399
d_215PHEPHEVALVALBB462 - 465401 - 404
d_216SERSERLYSLYSBB468 - 480407 - 419
d_217ALAALAALAALABB483 - 525422 - 464
d_218LEULEULEULEUBB527466
d_219VALVALLYSLYSBB529 - 592468 - 531
d_220ZNZNZNZNBH1001
d_221ADPADPADPADPBI1002

NCS oper: (Code: givenMatrix: (-0.723584207436, 0.554333162928, -0.411267114207), (0.550251653914, 0.103541046835, -0.828554385049), (-0.416712145388, -0.825829277816, -0.379943406032)Vector: 94. ...NCS oper: (Code: given
Matrix: (-0.723584207436, 0.554333162928, -0.411267114207), (0.550251653914, 0.103541046835, -0.828554385049), (-0.416712145388, -0.825829277816, -0.379943406032)
Vector: 94.9326918043, -19.9695992343, 36.5636117755)

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Components

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Protein / DNA chain , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent DNA helicase Q1 / DNA 3'-5' helicase Q1 / DNA helicase / RecQ-like type 1 / RecQ1 / DNA-dependent ATPase Q1 / RecQ ...DNA 3'-5' helicase Q1 / DNA helicase / RecQ-like type 1 / RecQ1 / DNA-dependent ATPase Q1 / RecQ protein-like 1


Mass: 60417.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL, RECQ1, RECQL1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): K-12 / References: UniProt: P46063, DNA 3'-5' helicase
#2: DNA chain DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 7260.647 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 10 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Malonate 0.1M pH 7 PEG 3350 12%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97847 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97847 Å / Relative weight: 1
ReflectionResolution: 3.69→77.83 Å / Num. obs: 17359 / % possible obs: 98.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 134.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.1
Reflection shellResolution: 3.69→3.76 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.628 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 862 / CC1/2: 0.871 / % 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: 3.69→77.83 Å / SU ML: 0.4728 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.1274
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 836 4.82 %
Rwork0.2436 16498 -
obs0.2444 17334 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 175.33 Å2
Refinement stepCycle: LAST / Resolution: 3.69→77.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8456 667 62 0 9185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329434
X-RAY DIFFRACTIONf_angle_d0.807112887
X-RAY DIFFRACTIONf_chiral_restr0.04811422
X-RAY DIFFRACTIONf_plane_restr0.00371513
X-RAY DIFFRACTIONf_dihedral_angle_d16.16423560
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.04845483526 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.920.40161090.36512486X-RAY DIFFRACTION90.32
3.92-4.230.30821320.31012739X-RAY DIFFRACTION99.9
4.23-4.650.29931350.25562759X-RAY DIFFRACTION99.79
4.65-5.330.2661640.25342753X-RAY DIFFRACTION99.93
5.33-6.710.30881480.27562803X-RAY DIFFRACTION99.97
6.71-77.830.18951480.19312958X-RAY DIFFRACTION99.74
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)
11.267259843240.980645155016-0.1140589869313.722491818211.566436976774.02467452546-0.112099269170.1643258159990.2845988917810.06712124649230.1788736423970.8070278271570.0431518630899-0.7530186864926.49320772481E-101.26184709151-0.0009879396493880.09433531199641.747262311380.4184769673671.7148522338326.6068231787-2.6183752267223.3019876159
23.05903369436-1.196865351930.3490674551932.997646967780.5771850101551.49915205329-0.01686583539950.5983075274140.462436852821-0.1681171900190.349478915303-0.150815685586-0.511125208340.0270090732199-3.02110653644E-111.65656196420.05251354248160.323221124731.563582768460.2953449379281.9971622814140.95335296812.934122654834.8092341381
34.48472972857-0.5304527034561.104662341821.387171037340.1159595375192.249311363290.04090003567630.1049675103480.7843726325891.239684310580.395542237094-1.14029333294-0.06653351840730.6699356627074.54563323109E-82.00396920830.0759758510352-0.3439532648561.58367961488-0.2513266198271.9268700193862.667275208510.55900442447.4543085581
43.46531723857-1.07132107459-3.14493764953.187663631491.827368627744.63497396963-0.308710235054-0.219050612201-0.460875033750.5888105859040.1078363084710.5098904004390.6150547003180.435210760689-1.41696897341E-81.424497028990.116702321788-0.1255621609711.498150006310.09145509374671.4802406233969.623616203-21.510026030827.2082456864
52.15485168087-2.19191338976-1.305014174681.818739023742.612652601174.48142167293-0.2029239553680.290529919541-0.155039349121-0.0246235879261-0.1126767091270.0740897843103-0.32227821276-0.406049813274-5.38079800427E-71.324834139470.0977889413581-0.002450518905241.555073994340.05741028265191.8666929333162.1598110502-10.551202361718.0709815544
65.71720046109-2.165577622572.462031543554.307211585671.679652567333.1329842912-0.210779333225-0.926633920325-0.6282954629190.08778462703510.824521500890.2861761455680.532807993809-0.5034163329482.8056101122E-71.79600136364-0.169575208186-0.07774537935531.551828005140.124962329551.7758964235257.426903422-41.98622044583.1878747996
72.78279009829-1.245846778851.963786149581.54215572332-0.2242193993031.539602008920.112609408254-0.383611481916-0.01935617232240.146619467560.353186458091-0.3863632193790.536686496943-0.199295943693-1.27108985105E-71.70565245751-0.204358188723-0.2110938944751.428302336810.05617022245131.8281218436756.9341752499-29.39838036441.99240031244
84.01787041968-0.8627408933041.842260835391.84603085113-0.4308258328743.606788759020.05585193952620.5685565654230.0608064074964-0.6912828212670.03011986945410.0506290812197-0.253258438737-0.5242415472974.99534269944E-81.87714485895-0.265812181324-0.1906324459951.795187670620.1373980052111.3702213579844.4012638051-22.4255888592-14.1147111696
92.640133360451.40123374497-2.297490720310.725720762573-1.159483450711.92838337152.416531016372.23234225123-0.509168061589-1.108143784143.024636222683.34951510281-0.4831884752860.01034937224510.1929307163424.074280609490.67131947016-0.8251541324245.750415310910.7764171567833.3352439261849.7700362696-24.602867081955.5618875286
100.0235305858719-0.07434271428150.1041802558920.155346676147-0.1901968638870.1151453623-0.0975300258139-2.040426555240.2986854387283.165857439292.80322957060.0456159563391.797605656230.765694843433-1.3572229859E-54.424056167711.238838079240.7765824260493.796948764170.9498718438874.1290571730544.4147367501-17.860620548446.375857384
110.144958367215-0.08002180620620.1778181560240.013168051715-0.0672928075906-0.0103960434858-0.257165395132-2.038988457551.311055390961.467999691610.389376502184-3.00521050087-3.58604181201-0.2217855924622.82418034359E-52.85719659955-0.2551015400550.1133535751483.55110020663-1.415947794374.0893434360846.7408554663-12.18520088456.8109202287
120.115008680602-0.1864417279910.09211511749360.1159143105-0.08791378656970.04954542194790.377192883325-0.635289740051.751377650091.210501787851.64321288342-0.373395979387-0.9503661826930.471153287508-2.23451278761E-52.749198697061.017413675820.1188403291033.841751176871.16288164694.4492657376430.5725067595-41.17445644827.50485326123
13-0.00693406869457-0.0033866143468-0.01121543560350.1715302085090.1762948183950.1160189120672.892659019040.778761041119-2.74539025328-0.117828175267-0.597898803495-0.151348845225.327388031851.635926152220.00467633336545.665901916631.80189126594-0.07634222873044.433748063870.8993773877533.2565733940420.1649548875-37.32997092367.42837942341
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 371 )AA62 - 3711 - 310
22chain 'A' and (resid 372 through 489 )AA372 - 489311 - 428
33chain 'A' and (resid 490 through 592 )AA490 - 592429 - 531
44chain 'B' and (resid 62 through 219 )BE62 - 2191 - 158
55chain 'B' and (resid 220 through 285 )BE220 - 285159 - 224
66chain 'B' and (resid 286 through 371 )BE286 - 371225 - 310
77chain 'B' and (resid 372 through 435 )BE372 - 435311 - 374
88chain 'B' and (resid 436 through 592 )BE436 - 592375 - 531
99chain 'C' and (resid 2 through 6 )CI2 - 6
1010chain 'C' and (resid 7 through 11 )CI7 - 11
1111chain 'C' and (resid 12 through 17 )CI12 - 17
1212chain 'D' and (resid 2 through 5 )DL2 - 5
1313chain 'D' and (resid 6 through 16 )DL6 - 16

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