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- PDB-9i22: Structure of Human helicase RecQ1- Myc G-quadruplex - ADP complex -

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Basic information

Entry
Database: PDB / ID: 9i22
TitleStructure of Human helicase RecQ1- Myc G-quadruplex - ADP complex
Components
  • ATP-dependent DNA helicase Q1
  • DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*AP*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 / : / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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*AP*GP*GP*GP*TP*GP*GP*GP*T)-3')
D: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,48019
Polymers135,9834
Non-polymers1,49715
Water00
1
A: ATP-dependent DNA helicase Q1
C: DNA (5'-D(P*GP*GP*GP*TP*GP*GP*GP*TP*AP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6659
Polymers67,9922
Non-polymers6737
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*AP*GP*GP*GP*TP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81510
Polymers67,9922
Non-polymers8238
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.195, 155.195, 126.841
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

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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*AP*GP*GP*GP*TP*GP*GP*GP*T)-3')


Mass: 7573.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 15 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.: 8 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

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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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: D-Malic acid 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: 2.42→77.6 Å / Num. obs: 40883 / % possible obs: 93.4 % / Redundancy: 25.2 % / Biso Wilson estimate: 64.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Net I/σ(I): 21.19
Reflection shellResolution: 2.42→2.58 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.875 / Mean I/σ(I) obs: 0.46 / Num. unique obs: 2045 / CC1/2: 0.623 / % possible all: 72.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→77.6 Å / SU ML: 0.3793 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.6294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2684 1984 4.85 %
Rwork0.2182 38895 -
obs0.2206 40879 68.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.98 Å2
Refinement stepCycle: LAST / Resolution: 2.42→77.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8456 750 76 0 9282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629537
X-RAY DIFFRACTIONf_angle_d1.156313040
X-RAY DIFFRACTIONf_chiral_restr0.07731438
X-RAY DIFFRACTIONf_plane_restr0.00751517
X-RAY DIFFRACTIONf_dihedral_angle_d16.89553619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.480.5778220.5096324X-RAY DIFFRACTION8.29
2.48-2.550.442530.3676952X-RAY DIFFRACTION23.91
2.55-2.620.4216770.33321433X-RAY DIFFRACTION36.13
2.62-2.70.3199690.33531308X-RAY DIFFRACTION32.76
2.71-2.80.37651160.34572149X-RAY DIFFRACTION54.21
2.8-2.910.44441370.3312528X-RAY DIFFRACTION62.85
2.91-3.050.39371450.36332907X-RAY DIFFRACTION72.29
3.05-3.210.34831620.3383369X-RAY DIFFRACTION83.95
3.21-3.410.37791850.28723861X-RAY DIFFRACTION95.6
3.41-3.670.32671710.24353430X-RAY DIFFRACTION84.65
3.67-4.040.3221990.21684072X-RAY DIFFRACTION100
4.04-4.620.22062140.16414092X-RAY DIFFRACTION100
4.63-5.830.21282150.16824135X-RAY DIFFRACTION100
5.83-77.60.19952190.18174335X-RAY DIFFRACTION99.91
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)
11.273604950660.382978327469-0.1088825046462.582885123521.097796121261.6988803229-0.03252224968380.1063242405480.0714394185732-0.242064549729-0.1840092088430.491247133405-0.0517693847655-0.2441693767-7.56353555272E-60.268049249927-0.02850589942370.02432325125580.3655578878970.06299269814440.35256037078921.1398629474-6.2781189004715.2675875582
21.04352504236-0.05650284307710.1385911150741.129493925070.6672274941940.6672813970230.01393918608930.101425716065-0.153398014322-0.2398347760110.225249241724-0.36826857024-0.2654884437830.2844857715834.91398620254E-60.366798265306-0.0549805679120.05572342886140.3857195640760.07324954171360.39543778318436.4804561097-2.1922702985413.4726971036
30.984248493132-0.06060909520180.4732933436561.59233033911-0.3850408301810.884246266029-0.0569357971493-0.9237809877850.09672759433760.5674859579250.05154575609570.41747544667-0.135845604773-0.30612178783-0.0004342247477770.439633085618-0.02720386866490.2654828205740.2028202864720.09791049354590.21763594247228.50813304315.1335643256545.6303650048
40.08974695215310.1504778865140.2071367729670.2911290299310.08637098781440.786595481794-0.0544575142961-0.08435687469810.1400797351870.0536288668066-0.08083293968420.152662912174-0.116543756582-0.09902670441414.77913578134E-80.4502570710710.03110571033750.08543437378680.260054479840.07408599806550.37963091382333.2654620966.8950710263635.2011902104
52.686957566710.001273974242840.7155554502951.917690473560.01565679597680.41008679165-0.0298235175692-0.1261632267610.3895026495370.336783914365-0.0849852320386-0.344359159699-0.04436665089460.1427743072760.0001259728686550.381420997267-0.0146697118104-0.007772319844010.251770654640.05515769284020.27966004201653.713259651812.937077736642.3359179991
61.32615438366-0.712837501015-1.689423295271.234583347941.655613627022.52818610872-0.33177459039-0.0794052757314-0.3316999822460.3350851488520.2281686494750.1161983874110.5685456431450.402487135828-0.00230408798390.4198036359440.08846591155170.04956746666190.3926743701930.1479319470510.47812600806169.6958346866-21.44533898228.6395135775
70.789618585032-0.852088807032-0.7913504401181.088069639451.255053768091.34154528756-0.0432995077580.0278446495397-0.186263590354-0.144161264445-0.04924311239310.122283671477-0.451339906856-0.336080905807-4.48923621484E-80.3757011307840.05572754303590.01397072819830.4792680840440.1033524839380.53464013779862.8471441486-11.417743970621.7937384015
81.56211672515-0.2592259231341.534726811912.419604447650.2686514990961.61805650003-0.130075703582-0.0544872654216-0.539668466830.1563635434450.26964565959-0.1102874537970.268430160622-0.1093667427330.0004110828906710.435304326120.01865495110840.06162726417650.329161412719-0.01643358351780.31920267534656.9605109651-42.30008651793.80846184806
90.2917919526870.2081213623350.2493348565050.4069870383260.0884557689020.143892438056-0.07483052218360.13979610216-0.09278543009690.1700203182240.264683976225-0.23304772193-0.02343210524570.05047046485761.31304225915E-70.4321740709390.01152675619040.0002259824187280.340709218517-0.1118064999020.42195094371359.7216242214-30.89568885425.78222758064
102.42927401204-0.07539121823360.2551034040972.06102410114-0.03099031115730.676064680674-0.1009550732380.317806561610.12812975877-0.473231838890.08423766295840.0627695742739-0.0278479911883-0.0325346829376-6.55323714847E-50.547808701454-0.05116012306490.01330110412250.38869756244-0.01176846709120.28696226241346.324177054-23.2133848321-10.9690261394
110.01379390109880.01852272866650.02429605578220.01843556908840.02557779193010.0431595052965-0.029127449115-0.04578849343460.337711674140.05284517991880.1067135989640.07322014988010.6055922095240.6903021283162.62940726012E-60.730355101507-0.0423760599813-0.1171352672281.066593465630.1274957583880.83675544948249.2309909859-24.72729316857.2158396944
120.0464068361661-0.0354379679895-0.006944271979470.0994882198831-0.1317230862440.2301878729320.547179393453-0.1711012745570.694473759632-0.675125763182-0.831883684242-1.090432046241.4166372103-0.02334460458260.0009977693462030.782308613972-0.05411954576720.1180671622690.7501375832980.2318693089330.70506008402245.6937062997-18.431008577345.7285194908
130.201076061470.0928023187617-0.1816824965890.0787128479999-0.08426027910650.148845506469-0.204861757844-0.7143157120590.636828369083-0.01814202798460.2694990731110.483035514496-0.8320924931860.3293049793361.89135326888E-60.937260800993-0.0188338670619-0.1712101065310.881753871017-0.2274153511911.1637920917145.0806800083-12.199226788958.2842198652
140.292313481846-0.0857439719230.1700650787010.0498756153783-0.007372018392730.123488362179-0.07707389966260.224109970517-0.15080747402-0.142067781542-0.238116404001-0.675652304330.6819148129951.143403097684.2413054091E-60.632903857856-0.02866367101860.1731940674150.901490171107-0.0819457453280.92235201153230.4267201509-39.90894664888.29366151858
150.302856529858-0.2863594939710.0398965016220.459453011209-0.326579581680.356736920412-0.105910474020.6614429047440.602204508422-1.03898699643-0.3002584474290.0956707270107-0.7429339278480.2139056723945.70710561913E-51.03431954825-0.130294129332-0.01232256860070.799560596775-0.03756622387690.79198508145220.9770604554-35.0843233795.22744308908
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 219 )AA62 - 2191 - 158
22chain 'A' and (resid 220 through 285 )AA220 - 285159 - 224
33chain 'A' and (resid 286 through 371 )AA286 - 371225 - 310
44chain 'A' and (resid 372 through 404 )AA372 - 404311 - 343
55chain 'A' and (resid 405 through 592 )AA405 - 592344 - 531
66chain 'B' and (resid 62 through 209 )BG62 - 2091 - 148
77chain 'B' and (resid 210 through 285 )BG210 - 285149 - 224
88chain 'B' and (resid 286 through 371 )BG286 - 371225 - 310
99chain 'B' and (resid 372 through 404 )BG372 - 404311 - 343
1010chain 'B' and (resid 405 through 592 )BG405 - 592344 - 531
1111chain 'C' and (resid 2 through 6 )CM2 - 6
1212chain 'C' and (resid 7 through 11 )CM7 - 11
1313chain 'C' and (resid 12 through 18 )CM12 - 18
1414chain 'D' and (resid 1 through 5 )DQ1 - 5
1515chain 'D' and (resid 6 through 18 )DQ6 - 18

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