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- PDB-4u7d: Structure of human RECQ-like helicase in complex with an oligonuc... -

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Basic information

Entry
Database: PDB / ID: 4u7d
TitleStructure of human RECQ-like helicase in complex with an oligonucleotide
Components
  • ATP-dependent DNA helicase Q1
  • DNA oligonucleotide
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / NUCLEAR PROTEIN / HYDROLASE / DNA STRAND ANNEALING / DNA BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
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 / DNA unwinding involved in DNA replication / replication fork processing / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination ...double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / DNA 3'-5' helicase / 3'-5' DNA helicase activity / DNA unwinding involved in DNA replication / replication fork processing / DNA helicase activity / isomerase activity / double-strand break repair via homologous recombination / chromosome / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm
Similarity search - Function
RQC domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...RQC domain / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleotide triphosphate hydrolases / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / ATP-dependent DNA helicase Q1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPike, A.C.W. / Zhang, Y. / Schnecke, C. / Cooper, C.D.O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Human RECQ1 helicase-driven DNA unwinding, annealing, and branch migration: Insights from DNA complex structures.
Authors: Pike, A.C. / Gomathinayagam, S. / Swuec, P. / Berti, M. / Zhang, Y. / Schnecke, C. / Marino, F. / von Delft, F. / Renault, L. / Costa, A. / Gileadi, O. / Vindigni, A.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q1
B: ATP-dependent DNA helicase Q1
C: ATP-dependent DNA helicase Q1
D: ATP-dependent DNA helicase Q1
P: DNA oligonucleotide
Q: DNA oligonucleotide
R: DNA oligonucleotide
S: DNA oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,06912
Polymers293,8078
Non-polymers2624
Water00
1
A: ATP-dependent DNA helicase Q1
B: ATP-dependent DNA helicase Q1
P: DNA oligonucleotide
Q: DNA oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0356
Polymers146,9044
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-36.5 kcal/mol
Surface area51800 Å2
MethodPISA
2
D: ATP-dependent DNA helicase Q1
R: DNA oligonucleotide
S: DNA oligonucleotide
hetero molecules

C: ATP-dependent DNA helicase Q1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0356
Polymers146,9044
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area4150 Å2
ΔGint-36.5 kcal/mol
Surface area51800 Å2
MethodPISA
3
C: ATP-dependent DNA helicase Q1
hetero molecules

D: ATP-dependent DNA helicase Q1
R: DNA oligonucleotide
S: DNA oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0356
Polymers146,9044
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4150 Å2
ΔGint-36.5 kcal/mol
Surface area51800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.380, 138.220, 207.581
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 67414.961 Da / Num. of mol.: 4 / Fragment: UNP residues 49-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL, RECQ1, RECQL1 / Plasmid: PNIC-CTHF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-PRARE2 / References: UniProt: P46063, DNA helicase
#2: DNA chain
DNA oligonucleotide


Mass: 6036.890 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.35 % / Description: Rod
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.18M potassium citrate, 17% (w/v) PEG3350, 5% (v/v) ethylene glycol, 0.1M bis-tris propane pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→83 Å / Num. obs: 40962 / % possible obs: 95.3 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.7
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1682)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1X

2v1x


Resolution: 3.4→39.9 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 42.82 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1951 4.77 %Random but taking into account pseudosymmetry
Rwork0.2051 ---
obs0.2138 40919 94.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16240 980 4 0 17224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717671
X-RAY DIFFRACTIONf_angle_d1.1424120
X-RAY DIFFRACTIONf_dihedral_angle_d17.4646449
X-RAY DIFFRACTIONf_chiral_restr0.0482767
X-RAY DIFFRACTIONf_plane_restr0.0052906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4004-3.49210.2521470.27292992X-RAY DIFFRACTION90
3.4921-3.59450.27711490.26593038X-RAY DIFFRACTION93
3.5945-3.71020.26831400.25553026X-RAY DIFFRACTION91
3.7102-3.84230.28861520.25663040X-RAY DIFFRACTION93
3.8423-3.99560.32751430.24722982X-RAY DIFFRACTION90
3.9956-4.17660.2821490.23173013X-RAY DIFFRACTION92
4.1766-4.39570.25991390.21252969X-RAY DIFFRACTION91
4.3957-4.66940.21991410.19833013X-RAY DIFFRACTION90
4.6694-5.02720.2421410.19562972X-RAY DIFFRACTION90
5.0272-5.52820.21461450.1932989X-RAY DIFFRACTION90
5.5282-6.31680.25751440.21382956X-RAY DIFFRACTION90
6.3168-7.9160.22511460.19392941X-RAY DIFFRACTION88
7.916-24.95250.23811480.15763016X-RAY DIFFRACTION90
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.2032-0.52240.7562.7344-0.52265.6714-0.227-0.62490.25920.96940.0717-0.1044-1.63710.4407-0.0131.7247-0.485-0.0820.90720.09530.8091Chain A RecA1 domain28.00092.107372.1414
23.1712-0.99232.69253.21620.36856.16440.0401-0.01920.08770.2313-0.21790.141-0.2474-0.0834-0.00850.69660.28260.05340.5818-0.15240.7875Chain B RecA1 domain4.63495.1013-34.657
33.96720.2827-0.52142.5748-2.40196.17760.45120.1721-0.0526-0.3701-0.38760.07121.17930.0534-0.00080.8841-0.02870.12360.57110.06680.897Chain C RecA1 domain33.679931.322929.9014
42.0827-0.4405-0.33942.83250.5835.80210.321-0.27190.03520.8291-0.25080.13141.0247-0.46760.01960.8061-0.48540.00880.8170.19520.7645Chain D RecA1 domain9.7213-40.103667.4081
50.00090.0947-0.29792.628-0.21871.29430.25140.081-0.4091-0.47280.0714-0.15661.4906-0.36260.00181.050.01670.05571.1060.0631.0778Chain PQ duplex15.6055-33.232318.2508
60.1479-0.01430.4934-0.03650.03171.3673-1.32330.03160.4121-0.4018-0.4010.33311.2145-0.4749-0.17271.31760.0096-0.35141.7375-0.1031.5556Chain RS duplex42.5164-11.125126.436
74.50291.85111.23922.40220.85764.27860.05380.11450.32960.0293-0.08610.0862-0.49160.2761-0.02580.4101-0.2246-0.00970.39830.09620.6166Chain A RecA2-Cterminus14.4311-12.289639.7224
83.6001-1.66441.1813.5552-2.04656.3007-0.2549-0.37480.38130.27960.2021-0.0382-0.6109-0.49820.00870.42460.00590.05290.6453-0.07580.6576Chain B RecA2-Cterminus17.0667-10.3221-1.8817
93.24720.7331.2885.3560.87065.78640.2374-0.6042-0.1450.6678-0.2202-0.11360.45350.48260.00061.153-0.48610.12010.80430.11490.635Chain C RecA2-Cterminus42.863247.598763.1974
102.640.95260.73943.71471.48833.96310.0894-0.9556-0.32180.5905-0.0229-0.07320.5769-0.3858-01.5526-0.42780.03541.56430.17850.7365Chain D RecA2-Cterminus19.9014-24.277100.6505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allchain 'D' and (resseq 283:592)D283 - 592
2X-RAY DIFFRACTION2chain 'B' and (resseq 63:282)
3X-RAY DIFFRACTION3chain 'C' and (resseq 63:282)
4X-RAY DIFFRACTION4chain 'D' and (resseq 63:282)
5X-RAY DIFFRACTION5chain 'P' or chain 'Q'
6X-RAY DIFFRACTION6chain 'R' or chain 'S'
7X-RAY DIFFRACTION7chain 'A' and (resseq 283:592)
8X-RAY DIFFRACTION8chain 'B' and (resseq 283:592)
9X-RAY DIFFRACTION9chain 'C' and (resseq 283:592)
10X-RAY DIFFRACTION10chain 'D' and (resseq 283:592)

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