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- PDB-9i16: Structure of RecQL-dsDNA-ADP-AlF4 complex from Bos taurus -

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Basic information

Entry
Database: PDB / ID: 9i16
TitleStructure of RecQL-dsDNA-ADP-AlF4 complex from Bos taurus
Components
  • (ATP-dependent DNA ...) x 2
  • DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-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 / double-strand break repair via homologous recombination / chromosome / DNA recombination / nucleic acid binding ...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 / double-strand break repair via homologous recombination / chromosome / DNA recombination / nucleic acid binding / DNA replication / hydrolase activity / nucleoplasm / 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 / DNA / DNA (> 10) / ATP-dependent DNA helicase / ATP-dependent DNA helicase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 16, 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
C: ATP-dependent DNA helicase
D: ATP-dependent DNA helicase
E: ATP-dependent DNA helicase
F: ATP-dependent DNA helicase
G: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
H: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
I: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
J: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
K: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
L: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,60647
Polymers396,19612
Non-polymers4,41035
Water00
1
A: ATP-dependent DNA helicase
B: ATP-dependent DNA helicase
G: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
H: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,94823
Polymers132,0714
Non-polymers1,87719
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP-dependent DNA helicase
D: ATP-dependent DNA helicase
I: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
J: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,31813
Polymers132,0554
Non-polymers1,2639
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: ATP-dependent DNA helicase
F: ATP-dependent DNA helicase
K: DNA (5'-D(P*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*C)-3')
L: DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,34111
Polymers132,0714
Non-polymers1,2707
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.559, 112.082, 181.788
Angle α, β, γ (deg.)90.000, 92.729, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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ATP-dependent DNA ... , 2 types, 6 molecules ABCEFD

#1: Protein
ATP-dependent DNA helicase


Mass: 60555.328 Da / Num. of mol.: 5
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
#2: Protein ATP-dependent DNA helicase


Mass: 60539.219 Da / Num. of mol.: 1
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: A0AAA9S5G9, DNA 3'-5' helicase

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DNA chain , 2 types, 6 molecules GIKHJL

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


Mass: 6341.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle)
#4: DNA chain DNA (5'-D(P*AP*GP*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*C)-3')


Mass: 4619.011 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Bos taurus (domestic cattle)

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Non-polymers , 5 types, 35 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#9: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: Tacsimate 5% HEPES 0.1M PEG MME 5000 10%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97851 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: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.82→29.89 Å / Num. obs: 78828 / % possible obs: 94.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 68.06 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.219 / Net I/σ(I): 5.3
Reflection shellResolution: 2.82→3.03 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.389 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3941 / CC1/2: 0.491 / % possible all: 67.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→29.89 Å / SU ML: 0.3247 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.7868
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2649 3927 4.99 %
Rwork0.2177 74781 -
obs0.22 78708 69.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.14 Å2
Refinement stepCycle: LAST / Resolution: 2.82→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25422 2016 235 0 27673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006828421
X-RAY DIFFRACTIONf_angle_d1.153138776
X-RAY DIFFRACTIONf_chiral_restr0.07784284
X-RAY DIFFRACTIONf_plane_restr0.01314540
X-RAY DIFFRACTIONf_dihedral_angle_d23.191710949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-2.850.4274100.418142X-RAY DIFFRACTION3.74
2.85-2.890.5985160.3927428X-RAY DIFFRACTION11
2.89-2.930.4571290.3601700X-RAY DIFFRACTION18.23
2.93-2.970.3982450.3291926X-RAY DIFFRACTION24.27
2.97-3.010.3425520.33861106X-RAY DIFFRACTION28.46
3.01-3.060.412540.31281293X-RAY DIFFRACTION33.5
3.06-3.10.3378800.30961498X-RAY DIFFRACTION38.71
3.1-3.150.33061090.29521637X-RAY DIFFRACTION43.6
3.15-3.210.34021070.29631923X-RAY DIFFRACTION49.85
3.21-3.270.32911320.30272064X-RAY DIFFRACTION54.64
3.27-3.330.34251280.29012279X-RAY DIFFRACTION59.53
3.33-3.40.31871590.29242487X-RAY DIFFRACTION65.2
3.4-3.470.30881580.26432701X-RAY DIFFRACTION70.77
3.47-3.550.30231670.25262913X-RAY DIFFRACTION76.62
3.55-3.640.28291770.25133141X-RAY DIFFRACTION81.74
3.64-3.740.31121630.25143384X-RAY DIFFRACTION87.36
3.74-3.850.31211610.23693566X-RAY DIFFRACTION92
3.85-3.970.27161720.22253742X-RAY DIFFRACTION96.81
3.97-4.110.2592050.21113845X-RAY DIFFRACTION99.8
4.11-4.280.27642100.2033868X-RAY DIFFRACTION99.78
4.28-4.470.25322170.19033821X-RAY DIFFRACTION99.88
4.47-4.710.21752010.18283882X-RAY DIFFRACTION99.95
4.71-50.24821700.19033870X-RAY DIFFRACTION99.9
5-5.390.2572250.19633881X-RAY DIFFRACTION100
5.39-5.920.23311980.21573885X-RAY DIFFRACTION100
5.92-6.770.28761810.23973893X-RAY DIFFRACTION100
6.77-8.50.23522190.20953913X-RAY DIFFRACTION99.93
8.5-29.890.20031820.16923993X-RAY DIFFRACTION99.43
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)
14.406281947181.87206100211-1.419782601393.12120294289-0.5981711391253.953260727-0.0686587474138-0.0210918663877-0.8170948707560.103368114517-0.07880462443450.2493219766250.711952001353-0.5034489451870.1427487061410.467381631746-0.185061906733-0.03630761753380.504223799240.0844212147770.5771556686583.73741856538-21.833313826340.1599793385
23.530295248220.5319038841822.433213555431.635695640831.388313400524.046637878540.189946382282-0.0138469346674-0.2674596849680.0803833112226-0.1208213167910.06512421506750.189181130524-0.19624845822-0.06664053135170.238733496986-0.0308405118390.03217834616760.260066459584-0.02553487014530.39545204866216.9072224742-22.69165130125.81040370427
33.00722989645-0.735457969799-1.503472848053.690643055610.9458167591113.566464713690.1432247620430.3630981780240.190056965004-0.123392261869-0.07115361462940.153496137511-0.0573205955876-0.218201159456-0.02113227561270.354584382240.0635185568881-0.007567411068550.2501730740230.07866518219950.59905900746480.0325896184-4.93325025199-25.3906488987
41.72490696490.989366940030.2055726076854.320672621960.1099480691990.6854059859240.05495358080740.05790139739790.1337874645870.13453665687-0.05854485571170.4389502598-0.174683384007-0.2077216669080.03271264801310.3539377780870.1282248869830.117023602290.3884232059870.02589284325920.66872633505153.947107837-23.5213294771-8.08530968196
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 - 2852 - 224
44chain 'B' and (resid 286 through 592 )BE286 - 592225 - 531

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