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- PDB-5lst: Crystal structure of the human RecQL4 helicase. -

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Basic information

Entry
Database: PDB / ID: 5lst
TitleCrystal structure of the human RecQL4 helicase.
ComponentsATP-dependent DNA helicase Q4
KeywordsHYDROLASE / RecQ4 / helicase / Rothmund-Thomson-Syndrome / RAPADILINO-Syndrome
Function / homology
Function and homology information


DNA/DNA annealing activity / telomeric D-loop binding / telomeric D-loop disassembly / DNA 3'-5' helicase / four-way junction helicase activity / bubble DNA binding / oxidized purine DNA binding / DNA duplex unwinding / DNA unwinding involved in DNA replication / isomerase activity ...DNA/DNA annealing activity / telomeric D-loop binding / telomeric D-loop disassembly / DNA 3'-5' helicase / four-way junction helicase activity / bubble DNA binding / oxidized purine DNA binding / DNA duplex unwinding / DNA unwinding involved in DNA replication / isomerase activity / telomere maintenance / helicase activity / double-strand break repair via homologous recombination / chromosome / DNA replication / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA replication/checkpoint protein / DNA replication and checkpoint protein / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 ...DNA replication/checkpoint protein / DNA replication and checkpoint protein / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Q4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsKaiser, S. / Sauer, F. / Kisker, C.
CitationJournal: Nat Commun / Year: 2017
Title: The structural and functional characterization of human RecQ4 reveals insights into its helicase mechanism.
Authors: Kaiser, S. / Sauer, F. / Kisker, C.
History
DepositionSep 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4792
Polymers76,4141
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.001, 131.001, 96.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ATP-dependent DNA helicase Q4 / DNA helicase / RecQ-like type 4 / RecQ4 / RTS / RecQ protein-like 4


Mass: 76413.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL4, RECQ4 / Plasmid: pETM-22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): star / References: UniProt: O94761, DNA helicase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.12 Å3/Da / Density % sol: 60.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Imidazole, Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.75→44.34 Å / Num. obs: 25149 / % possible obs: 99.8 % / Redundancy: 14.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.7
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.894 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.75→44.34 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.36
RfactorNum. reflection% reflection
Rfree0.2314 2459 5.12 %
Rwork0.1828 --
obs0.1853 47984 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 108.8 Å2
Refinement stepCycle: LAST / Resolution: 2.75→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 1 0 4693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044792
X-RAY DIFFRACTIONf_angle_d0.6816510
X-RAY DIFFRACTIONf_dihedral_angle_d17.6551757
X-RAY DIFFRACTIONf_chiral_restr0.047753
X-RAY DIFFRACTIONf_plane_restr0.006854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-2.80310.35071400.32822578X-RAY DIFFRACTION100
2.8031-2.86030.35881340.31462524X-RAY DIFFRACTION100
2.8603-2.92250.28911390.2872519X-RAY DIFFRACTION100
2.9225-2.99040.39191320.28842529X-RAY DIFFRACTION100
2.9904-3.06520.33691650.26352555X-RAY DIFFRACTION100
3.0652-3.14810.28251190.26212514X-RAY DIFFRACTION100
3.1481-3.24070.3481390.25562575X-RAY DIFFRACTION100
3.2407-3.34520.34211120.25382507X-RAY DIFFRACTION100
3.3452-3.46480.36061230.22772559X-RAY DIFFRACTION100
3.4648-3.60340.25171500.20272521X-RAY DIFFRACTION100
3.6034-3.76730.23071330.19482539X-RAY DIFFRACTION100
3.7673-3.96580.27781550.18562534X-RAY DIFFRACTION100
3.9658-4.21410.16951470.16672489X-RAY DIFFRACTION100
4.2141-4.53920.21981450.14522496X-RAY DIFFRACTION99
4.5392-4.99550.19051230.14252512X-RAY DIFFRACTION99
4.9955-5.7170.26031410.17242522X-RAY DIFFRACTION99
5.717-7.19780.19081320.18982522X-RAY DIFFRACTION99
7.1978-44.34620.17161300.14792530X-RAY DIFFRACTION99
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)
17.68462.84191.74046.67242.71146.1540.3951-0.3081-0.93390.107-0.3063-0.29360.4534-0.4587-0.11740.6797-0.00470.07350.62760.06610.832454.6387-32.78177.1764
22.655-0.6235-0.8613.32480.4092.492-0.0524-0.0078-0.09480.1703-0.00540.073-0.0352-0.22130.06270.7261-0.0747-0.0260.55030.02440.74941.2115-12.827615.9272
39.049-1.7181-0.31850.78270.3820.91650.0314-0.40280.0081-0.07-0.0057-0.26770.0805-0.0352-0.01130.83740.0897-0.0670.54210.07550.701155.0923-7.223411.2897
42.9699-1.35721.19541.2011-0.57370.7598-0.0405-0.08320.0225-0.07440.0805-0.1610.04140.012-0.06760.86410.08280.01670.7654-0.04120.911775.3541-17.607313.5949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 449 through 630 )
2X-RAY DIFFRACTION2chain 'A' and (resid 631 through 771 )
3X-RAY DIFFRACTION3chain 'A' and (resid 772 through 884 )
4X-RAY DIFFRACTION4chain 'A' and (resid 885 through 1111 )

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