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- PDB-7xut: Crystal structure of RPA70N-WRN fusion -

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Basic information

Entry
Database: PDB / ID: 7xut
TitleCrystal structure of RPA70N-WRN fusion
Componentsfusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase
KeywordsDNA BINDING PROTEIN / RPA / RPA70N / WRN
Function / homology
Function and homology information


3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / protein localization to chromosome / telomeric D-loop binding / regulation of growth rate / DNA replication factor A complex / telomere maintenance via semi-conservative replication ...3'-flap-structured DNA binding / positive regulation of strand invasion / telomeric G-quadruplex DNA binding / positive regulation of hydrolase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / protein localization to chromosome / telomeric D-loop binding / regulation of growth rate / DNA replication factor A complex / telomere maintenance via semi-conservative replication / : / t-circle formation / telomeric D-loop disassembly / Y-form DNA binding / G-quadruplex DNA binding / MutLalpha complex binding / bubble DNA binding / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / Impaired BRCA2 binding to PALB2 / protein localization to site of double-strand break / Removal of the Flap Intermediate / G-rich strand telomeric DNA binding / Processive synthesis on the C-strand of the telomere / protein localization to nucleolus / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / response to UV-C / : / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / 3'-5' DNA helicase activity / exonuclease activity / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / DNA metabolic process / Impaired BRCA2 binding to RAD51 / DNA synthesis involved in DNA repair / replication fork processing / site of DNA damage / : / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / Regulation of HSF1-mediated heat shock response / HSF1 activation / telomere maintenance via telomerase / mismatch repair / SUMOylation of DNA damage response and repair proteins / Activation of ATR in response to replication stress / DNA helicase activity / four-way junction DNA binding / 3'-5' exonuclease activity / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / cellular response to starvation / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / meiotic cell cycle / determination of adult lifespan / isomerase activity / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / cellular response to gamma radiation / base-excision repair / G2/M DNA damage checkpoint / PML body / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular senescence / double-strand break repair / single-stranded DNA binding / chromosome / site of double-strand break / manganese ion binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / response to oxidative stress / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity
Similarity search - Function
Helicase Helix-turn-helix domain / Helix-turn-helix domain / Replication factor-A protein 1, N-terminal domain / RQC domain / RQC / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / RQC domain ...Helicase Helix-turn-helix domain / Helix-turn-helix domain / Replication factor-A protein 1, N-terminal domain / RQC domain / RQC / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / RQC domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / HRDC domain superfamily / 3'-5' exonuclease / 3'-5' exonuclease / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / 3'-5' exonuclease domain / OB-fold nucleic acid binding domain / HRDC-like superfamily / Nucleic acid-binding proteins / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWu, Y.Y. / Zang, N. / Fu, W.M. / Zhou, C.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, China) China
CitationJournal: Elife / Year: 2023
Title: Structural characterization of human RPA70N association with DNA damage response proteins.
Authors: Wu, Y. / Fu, W. / Zang, N. / Zhou, C.
History
DepositionMay 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_DOI ..._citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase
B: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase


Theoretical massNumber of molelcules
Total (without water)30,9702
Polymers30,9702
Non-polymers00
Water4,414245
1
A: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase

B: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase


Theoretical massNumber of molelcules
Total (without water)30,9702
Polymers30,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area2940 Å2
ΔGint-8 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.936, 58.609, 111.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fusion protein of Replication protein A 70 kDa DNA-binding subunit and Werner syndrome ATP-dependent helicase / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / ...RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein / DNA helicase / RecQ-like type 3 / RecQ3 / Exonuclease WRN / RecQ protein-like 2


Mass: 15484.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70, WRN, RECQ3, RECQL2 / Production host: Escherichia coli (E. coli)
References: UniProt: P27694, UniProt: Q14191, DNA helicase, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 1.76 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.6→31.59 Å / Num. obs: 54591 / % possible obs: 99.78 % / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.09657 / Rpim(I) all: 0.04187 / Net I/σ(I): 13.82
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.152 / Num. unique obs: 2870 / CC1/2: 0.98 / Rpim(I) all: 0.0641 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20rc1_4392refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5eay

5eay


Resolution: 1.6→31.59 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 2749 5.04 %
Rwork0.1793 51842 -
obs0.181 54591 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.52 Å2 / Biso mean: 21.5343 Å2 / Biso min: 4.81 Å2
Refinement stepCycle: final / Resolution: 1.6→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 0 245 2370
Biso mean---27.63 -
Num. residues----276
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.27391500.213425802730100
1.63-1.660.28491290.197826132742100
1.66-1.690.25731300.201826292759100
1.69-1.720.20371560.204926352791100
1.72-1.760.24411470.193225672714100
1.76-1.80.28321370.19992615275299
1.8-1.850.20881340.1842586272099
1.85-1.90.24061500.18812516266698
1.9-1.950.19331500.17942617276799
1.95-2.020.22921600.18152565272599
2.02-2.090.20661600.16932606276699
2.09-2.170.20041220.17572606272899
2.17-2.270.23011210.18322567268899
2.27-2.390.26491130.17912587270097
2.39-2.540.2046950.18492655275099
2.54-2.740.23011330.18672583271699
2.74-3.010.23241320.19152601273399
3.01-3.450.19731300.17532554268498
3.45-4.340.18391440.15462588273299
4.34-31.590.18861560.17312572272899
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)
18.675-4.05560.4732.5226-0.43350.23190.155-0.3266-0.698-0.0485-0.0570.65730.1637-1.0158-0.11720.1397-0.0405-0.01460.2966-0.00210.2435-1.2563.77320.349
21.4530.1082-0.01931.71780.19071.09990.0756-0.0188-0.00760.0397-0.0427-0.1786-0.02230.0498-0.05170.093-0.0116-0.00210.0984-0.00560.10019.9339.00919.15
32.6474-0.0183-1.50181.4932.14944.86130.73430.83371.3446-1.4347-0.6204-1.1363-1.83940.9335-0.58350.8587-0.02280.20240.58290.05520.692815.93725.9525.289
41.05980.5059-0.56031.4299-0.98311.3295-0.105-0.0029-0.1399-0.13190.0979-0.10770.1493-0.0166-0.0150.0805-0.00480.00280.1194-0.0030.09146.83714.79218.928
52.4035-0.5339-0.60071.2269-0.351.82210.14190.05760.3547-0.4083-0.0563-0.5340.04650.4107-0.01860.2498-0.00150.03930.11720.03040.103812.96114.8286.218
62.65050.9886-1.82431.5905-1.40995.7567-0.01470.3672-0.1087-0.6565-0.0983-0.065-0.12590.2612-0.0220.23250.0079-0.02310.21710.00460.13472.30914.1295.481
72.00750.40041.45650.6751-0.42571.8844-0.0625-0.0342-0.011-0.0380.0074-0.0803-0.14740.0690.07340.1270.030.00260.164-0.02340.13616.60310.77217.757
82.10960.30080.52191.9251-0.3341.94030.0930.0191-0.0802-0.0851-0.002-0.15130.06290.0835-0.05350.10110.02760.01520.1196-0.01330.104811.5728.49312.071
90.668-0.0255-0.84231.39020.6891.2698-0.00510.03270.115-0.0438-0.04010.168-0.0721-0.1994-0.0630.0817-0.0147-0.0050.140.00640.1022-1.70712.98918.364
102.9448-0.282-0.67553.5668-1.04542.85350.24160.19570.6442-0.1436-0.08430.0799-0.3851-0.1319-0.21730.2149-0.00510.05960.1427-0.00260.211.45127.89319.245
114.1410.8509-0.67663.6291-1.12782.6258-0.0438-0.2139-0.00060.0542-0.0065-0.2685-0.24210.10780.01750.15470.0144-0.02510.1044-0.00560.13839.982-7.24619.403
121.59761.41210.62682.1418-0.09051.4932-0.0685-0.03450.1218-0.0680.0073-0.0005-0.1289-0.14160.08060.13210.00850.0020.13390.02550.12887.811-14.4413.053
130.81230.57780.27751.67691.28281.03640.22320.51220.4588-1.2077-0.0939-0.0254-0.45810.14390.05980.31380.0025-0.02010.19070.01060.19510.398-34.0345.649
141.2469-0.0053-0.34782.5729-0.54871.2895-0.00110.0269-0.1042-0.6028-0.0384-0.0184-0.0206-0.22850.04150.17710.01310.00130.09580.020.10036.957-19.3510.958
152.65860.48672.60651.94960.46.83830.09890.4297-0.1333-1.3377-0.1022-0.8290.5469-0.0040.02660.44510.01350.11250.24480.040.259514.808-19.2353.416
162.83870.4274-0.21064.21020.50352.5546-0.01770.03850.2362-0.3683-0.02010.42460.2209-0.32410.09940.18620.0171-0.04360.1543-0.00550.15331.969-14.24312.318
170.4289-0.45370.08882.3174-0.56771.2269-0.0058-0.00450.0532-0.1113-0.1746-0.9686-0.12670.37640.03750.1088-0.00250.08140.19160.05540.369518.322-15.35515.933
183.4243-1.4499-0.23142.2942-0.96940.6353-0.07650.2486-0.3483-0.0042-0.0273-0.26710.29650.1750.04050.12860.0128-0.01060.1536-0.0160.224917.056-31.26918.79
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:8 )A1 - 8
2X-RAY DIFFRACTION2( CHAIN A AND RESID 9:32 )A9 - 32
3X-RAY DIFFRACTION3( CHAIN A AND RESID 33:41 )A33 - 41
4X-RAY DIFFRACTION4( CHAIN A AND RESID 42:55 )A42 - 55
5X-RAY DIFFRACTION5( CHAIN A AND RESID 56:67 )A56 - 67
6X-RAY DIFFRACTION6( CHAIN A AND RESID 68:75 )A68 - 75
7X-RAY DIFFRACTION7( CHAIN A AND RESID 76:91 )A76 - 91
8X-RAY DIFFRACTION8( CHAIN A AND RESID 92:103 )A92 - 103
9X-RAY DIFFRACTION9( CHAIN A AND RESID 104:119 )A104 - 119
10X-RAY DIFFRACTION10( CHAIN A AND RESID 120:449 )A120 - 449
11X-RAY DIFFRACTION11( CHAIN B AND RESID 1:16 )B1 - 16
12X-RAY DIFFRACTION12( CHAIN B AND RESID 17:33 )B17 - 33
13X-RAY DIFFRACTION13( CHAIN B AND RESID 34:40 )B34 - 40
14X-RAY DIFFRACTION14( CHAIN B AND RESID 41:67 )B41 - 67
15X-RAY DIFFRACTION15( CHAIN B AND RESID 68:75 )B68 - 75
16X-RAY DIFFRACTION16( CHAIN B AND RESID 76:103 )B76 - 103
17X-RAY DIFFRACTION17( CHAIN B AND RESID 104:119 )B104 - 119
18X-RAY DIFFRACTION18( CHAIN B AND RESID 120:451 )B120 - 451

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