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- PDB-2wwy: Structure of human RECQ-like helicase in complex with a DNA substrate -

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Basic information

Entry
Database: PDB / ID: 2wwy
TitleStructure of human RECQ-like helicase in complex with a DNA substrate
Components
  • 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'
  • ATP-DEPENDENT DNA HELICASE Q1
  • DNA OLIGO (27BP)
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / NUCLEAR PROTEIN / HYDROLASE / DNA STRAND ANNEALING / DNA-BINDING
Function / homology
Function and homology information


double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity ...double-stranded DNA helicase activity / DNA/DNA annealing activity / four-way junction helicase activity / mediator complex / DNA 3'-5' helicase / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / 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 / DEAD/DEAH box helicase domain / 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 / DEAD/DEAH box helicase domain / 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: 2.9 Å
AuthorsPike, A.C.W. / Zhang, Y. / Schnecke, C. / Chaikuad, A. / Krojer, T. / Cooper, C.D.O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Pike, A.C.W. / Zhang, Y. / Schnecke, C. / Chaikuad, A. / Krojer, T. / Cooper, C.D.O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gileadi, O.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Recq1 Helicase-Driven DNA Unwinding, Annealing, and Branch Migration: Insights from DNA Complex Structures
Authors: Pike, A.C.W. / Zhang, Y. / Schnecke, C. / Chaikuad, A. / Krojer, T. / Cooper, C.D.O. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Gileadi, O.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of the Human Recq1 Helicase Reveals a Putative Strand-Separation Pin.
Authors: Pike, A.C.W. / Shrestha, B. / Popuri, V. / Burgess-Brown, N. / Muzzolini, L. / Costantini, S. / Vindigni, A. / Gileadi, O.
History
DepositionOct 30, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references / Derived calculations / Version format compliance
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Apr 22, 2015Group: Database references
Revision 1.4Sep 16, 2015Group: Derived calculations / Source and taxonomy
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
O: DNA OLIGO (27BP)
P: 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'
Q: DNA OLIGO (27BP)
R: DNA OLIGO (27BP)
S: 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'
T: DNA OLIGO (27BP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,20316
Polymers175,5648
Non-polymers6398
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-104.25 kcal/mol
Surface area60680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.333, 174.218, 100.229
Angle α, β, γ (deg.)90.00, 93.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESID 76:92 OR RESID 94: 149 OR...
211CHAIN B AND (RESID 76:92 OR RESID 94: 149 OR...
112CHAIN A AND (RESID 65:75 OR RESID 150: 199 OR...
212CHAIN B AND (RESID 65:75 OR RESID 150: 199 OR...

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.57491, 0.81412, 0.0818), (0.81396, -0.57924, 0.04427), (0.08342, 0.04113, -0.99566)
Vector: -0.77837, -4.74743, 59.55817)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATP-DEPENDENT DNA HELICASE Q1 / RECQ LIKE DNA HELICASE / DNA-DEPENDENT ATPASE Q1


Mass: 67384.938 Da / Num. of mol.: 2 / Fragment: RESIDUES 49-616
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: P46063, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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DNA chain , 2 types, 6 molecules OQRTPS

#2: DNA chain
DNA OLIGO (27BP)


Mass: 8210.268 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'


Mass: 3976.599 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 92 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.5 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M SOUDIUM SULPHATE, 20% PEG3350, 10% ETHYLENE GLYCOL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→49.5 Å / Num. obs: 44075 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 75.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V1X

2v1x


Resolution: 2.9→43.38 Å / SU ML: 0.47 / σ(F): 1.95 / Phase error: 26.19 / Stereochemistry target values: ML / Details: A SINGLE BFACTOR GROUP REFINED PER RESIDUE
RfactorNum. reflection% reflection
Rfree0.236 2217 5.04 %
Rwork0.198 --
obs0.2 44020 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.21 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 79 Å2
Baniso -1Baniso -2Baniso -3
1--1.2551 Å20 Å2-3.5775 Å2
2--15.9334 Å20 Å2
3----14.6783 Å2
Refinement stepCycle: LAST / Resolution: 2.9→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8235 1378 30 84 9727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119971
X-RAY DIFFRACTIONf_angle_d1.44113761
X-RAY DIFFRACTIONf_dihedral_angle_d21.293696
X-RAY DIFFRACTIONf_chiral_restr0.091559
X-RAY DIFFRACTIONf_plane_restr0.0041519
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2695X-RAY DIFFRACTIONPOSITIONAL
12B2695X-RAY DIFFRACTIONPOSITIONAL0.049
21A1211X-RAY DIFFRACTIONPOSITIONAL
22B1211X-RAY DIFFRACTIONPOSITIONAL0.512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9004-2.96340.34471360.30992473X-RAY DIFFRACTION95
2.9634-3.03240.34071300.29742640X-RAY DIFFRACTION100
3.0324-3.10820.31021530.282563X-RAY DIFFRACTION100
3.1082-3.19220.34971230.2682636X-RAY DIFFRACTION100
3.1922-3.28610.28811120.26242652X-RAY DIFFRACTION100
3.2861-3.39210.28331370.24752622X-RAY DIFFRACTION100
3.3921-3.51330.30841110.22922630X-RAY DIFFRACTION100
3.5133-3.65390.24891280.21472650X-RAY DIFFRACTION100
3.6539-3.82010.23091500.19852585X-RAY DIFFRACTION100
3.8201-4.02140.25031450.19532620X-RAY DIFFRACTION100
4.0214-4.27310.20651620.17342600X-RAY DIFFRACTION100
4.2731-4.60270.19921580.15152594X-RAY DIFFRACTION100
4.6027-5.06530.17031440.14372618X-RAY DIFFRACTION100
5.0653-5.79670.21191450.14972628X-RAY DIFFRACTION100
5.7967-7.29760.21831370.17442651X-RAY DIFFRACTION100
7.2976-43.38930.1841460.15462641X-RAY DIFFRACTION100
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)
11.90970.01451.09172.0055-1.3445.0266-0.203-0.1266-0.06470.48850.2430.1095-1.2663-0.6345-0.00020.99810.27870.08650.5285-0.03530.48194.572726.35139.1777
22.8598-0.88850.30722.0552-0.03912.4986-0.0979-0.19490.05920.09940.1242-0.0158-0.31560.0484-0.00010.0845-0.03250.00570.11080.03590.180420.4451-3.025661.0951
32.19570.5061-0.70991.9234-2.09026.64010.12860.1406-0.0519-0.2874-0.0885-0.03480.83950.0286-0.00010.53020.00960.00390.4433-0.12440.381426.5787-14.333721.4342
41.0601-0.34480.18623.59550.63383.0714-0.1846-0.0413-0.056-0.16610.00260.0772-0.28340.021100.47040.04660.00170.5341-0.02070.407813.236516.61010.2624
52.4660.1177-0.5832.75561.69691.60830.5148-0.6482-1.05940.18580.22610.90481.0285-0.05270.00120.7227-0.1036-0.12280.74290.32680.848917.7676-30.634263.5213
62.74510.7769-1.05392.31341.7012.22590.07130.9142-0.2622-0.43750.51022.1596-1.0197-0.2879-0.00031.14710.0533-0.34611.48790.15391.033-10.172528.3556-1.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 63:280)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 281:592)
3X-RAY DIFFRACTION3CHAIN B AND (RESID 64:285)
4X-RAY DIFFRACTION4CHAIN B AND (RESID 286:593)
5X-RAY DIFFRACTION5CHAIN O OR CHAIN P OR CHAIN Q
6X-RAY DIFFRACTION6CHAIN R OR CHAIN S OR CHAIN T

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