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- PDB-3aaf: Structure of WRN RQC domain bound to double-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 3aaf
TitleStructure of WRN RQC domain bound to double-stranded DNA
Components
  • DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3')
  • Werner syndrome ATP-dependent helicase
KeywordsDNA BINDING PROTEIN/DNA / HELIX-TURN-HELIX / WINGED-HELIX / PROTEIN-DNA COMPLEX / DNA-binding / Helicase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / t-circle formation ...3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / regulation of growth rate / telomere maintenance via semi-conservative replication / t-circle formation / G-quadruplex DNA unwinding / telomeric D-loop disassembly / Y-form DNA binding / four-way junction helicase activity / G-quadruplex DNA binding / MutLalpha complex binding / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / Removal of the Flap Intermediate from the C-strand / protein localization to nucleolus / DNA 3'-5' helicase / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / exonuclease activity / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA metabolic process / DNA synthesis involved in DNA repair / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / isomerase activity / 3'-5' exonuclease activity / cellular response to starvation / telomere maintenance / replication fork / determination of adult lifespan / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / cellular response to gamma radiation / cellular senescence / double-strand break repair / chromosome / manganese ion binding / Processing of DNA double-strand break ends / DNA replication / Regulation of TP53 Activity through Phosphorylation / response to oxidative stress / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nuclear speck / centrosome / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / magnesium ion binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / HRDC-like superfamily / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKitano, K. / Hakoshima, T.
CitationJournal: Structure / Year: 2010
Title: Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN
Authors: Kitano, K. / Kim, S.Y. / Hakoshima, T.
History
DepositionNov 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Werner syndrome ATP-dependent helicase
B: Werner syndrome ATP-dependent helicase
C: DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3')
D: DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3816
Polymers39,2634
Non-polymers1182
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-31 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.077, 84.077, 145.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-83-

HOH

21A-290-

HOH

31A-335-

HOH

41B-258-

HOH

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Components

#1: Protein Werner syndrome ATP-dependent helicase / Werner syndrome protein / WRN


Mass: 15351.547 Da / Num. of mol.: 2 / Fragment: RecQ C-terminal (RQC) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-5X-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus RIL
References: UniProt: Q14191, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: DNA chain DNA (5'-D(*AP*CP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*GP*T)-3')


Mass: 4279.804 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.2762.38
2
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9
Details: 20% PEG 4000, 0.2M sodium acetate, 0.1M CAPS-NaOH, pH 9, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2902
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL41XU21.0057, 1.0090, 1.0257
Detector
TypeIDDetectorDate
Bruker DIP-60401CCDSep 30, 2007
RAYONIX MX225HE2CCDJul 19, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.00571
31.0091
41.02571
ReflectionResolution: 1.9→20 Å / Num. obs: 41719 / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 6.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.336 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24354 2107 5.1 %RANDOM
Rwork0.21177 ---
obs0.21339 39605 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.246 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2--1.6 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 568 8 338 2690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222460
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4092.2413426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18823.02386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28115334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8151514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021660
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.21073
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21627
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6141.51112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03821716
X-RAY DIFFRACTIONr_scbond_it1.49131750
X-RAY DIFFRACTIONr_scangle_it2.3084.51710
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 158 -
Rwork0.254 2812 -
obs--98.93 %
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)
11.1367-0.3664-0.54040.70540.02816.51990.0092-0.0319-0.14770.04020.058-0.11080.83570.3218-0.06720.01130.0812-0.0385-0.1277-0.0313-0.071346.420429.716840.1429
20.4814-0.40950.57561.0280.76746.485-0.01660.02780.1368-0.0507-0.16420.1981-0.5646-0.65930.1808-0.130.0802-0.0017-0.0606-0.0433-0.084571.4974.65829.3888
34.0973-4.5257-0.71565.49940.57830.2149-0.10120.0535-0.27630.1449-0.0364-0.0562-0.1017-0.01690.13760.27620.2619-0.14880.0872-0.08110.059261.730119.161926.3057
48.3053-8.80222.19619.3371-2.38270.9492-0.4467-0.4238-0.35160.56480.57620.3865-0.3518-0.5307-0.12960.05170.2069-0.05560.126-0.07930.020960.741119.985723.2908
50.9845-0.9577-0.68210.93150.66350.4726-0.01210.13050.00020.0276-0.11250.0221-0.0558-0.19640.12460.15950.076-0.03850.156-0.04230.122959.958516.617723.6393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A956 - 1064
2X-RAY DIFFRACTION2B956 - 1064
3X-RAY DIFFRACTION3C1 - 14
4X-RAY DIFFRACTION4D1 - 14
5X-RAY DIFFRACTION5A1
6X-RAY DIFFRACTION5A4 - 305

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