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- PDB-7xv1: Crystal structure of RPA70N-HelB fusion -

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Basic information

Entry
Database: PDB / ID: 7xv1
TitleCrystal structure of RPA70N-HelB fusion
Components
  • DNA helicase B
  • Replication protein A 70 kDa DNA-binding subunitDNA replication
KeywordsDNA BINDING PROTEIN / RPA / RPA70N / HelB
Function / homology
Function and homology information


regulation of DNA double-strand break processing / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 5'-3' DNA helicase activity ...regulation of DNA double-strand break processing / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / protein localization to site of double-strand break / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 5'-3' DNA helicase activity / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / single-stranded DNA helicase activity / DNA replication, synthesis of primer / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / negative regulation of double-strand break repair via homologous recombination / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / Activation of the pre-replicative complex / HSF1 activation / Regulation of HSF1-mediated heat shock response / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Gap-filling DNA repair synthesis and ligation in GG-NER / Translesion synthesis by POLI / meiotic cell cycle / nucleotide-excision repair / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / PML body / DNA-templated DNA replication / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded DNA binding / site of double-strand break / Processing of DNA double-strand break ends / DNA recombination / DNA helicase / Regulation of TP53 Activity through Phosphorylation / DNA replication / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / DNA damage response / protein-containing complex binding / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / Replication factor A, C-terminal / Replication factor-A C terminal domain ...Replication factor-A protein 1, N-terminal domain / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / : / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / Replication factor A, C-terminal / Replication factor-A C terminal domain / AAA domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Replication protein A 70 kDa DNA-binding subunit / DNA helicase B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 20, 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

Downloads & links

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Assembly

Deposited unit
A: Replication protein A 70 kDa DNA-binding subunit
B: DNA helicase B


Theoretical massNumber of molelcules
Total (without water)16,4942
Polymers16,4942
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-7 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.333, 50.333, 126.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Replication protein A 70 kDa DNA-binding subunit / DNA replication / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13187.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70 / Production host: Escherichia coli (E. coli) / References: UniProt: P27694
#2: Protein/peptide DNA helicase B / hDHB


Mass: 3306.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HELB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NG08, DNA helicase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / Details: 20% PEG3350 200 mM Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→24.68 Å / Num. obs: 28713 / % possible obs: 99.83 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06153 / Rpim(I) all: 0.0188 / Net I/σ(I): 26.49
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.4831 / Num. unique obs: 2524 / CC1/2: 0.982 / Rpim(I) all: 0.14 / % 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: 1.8→24.68 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1479 5.15 %
Rwork0.1967 27234 -
obs0.1977 28713 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.34 Å2 / Biso mean: 35.3766 Å2 / Biso min: 17.34 Å2
Refinement stepCycle: final / Resolution: 1.8→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 93 1223
Biso mean---41.16 -
Num. residues----146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.2681020.227925242626100
1.86-1.920.25951350.220524742609100
1.92-20.24571470.201924532600100
2-2.090.24271350.202925042639100
2.09-2.20.20881320.204224622594100
2.2-2.340.25341340.207524702604100
2.34-2.520.24681260.205725042630100
2.52-2.770.23481490.226524602609100
2.77-3.180.24821370.20824812618100
3.18-40.20621330.182324702603100
4-24.680.17861490.18152432258198
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)
11.38550.1539-0.05680.63510.94681.1512-0.06880.22870.1597-0.78720.1372-0.48140.0920.23530.00010.2928-0.02850.0080.21710.00760.247713.2686-9.701110.9409
21.61910.26880.66463.56770.27532.21060.0317-0.0861-0.10050.2641-0.06430.13080.0086-0.09350.00040.220.0015-0.01050.19350.00190.20232.1134-13.259415.3778
31.17220.64820.56710.83360.19861.0028-0.0874-0.14330.36210.24210.0880.7529-0.0853-0.4252-0.00280.31210.09610.06680.2996-0.00020.4299-4.4006-8.424320.6677
42.9177-0.18471.32980.8363-1.33431.68140.0693-0.0881-0.03530.5571-0.09160.0833-0.1316-0.1158-00.27950.00440.02030.1493-0.00670.1716.4253-14.185520.5142
52.06011.16080.80050.65580.26970.85320.02720.5023-0.1881-0.3709-0.09240.73930.1331-0.28-0.00380.41570.0745-0.04840.29760.03030.21573.4919-7.94676.1041
60.55780.06940.00280.19-0.14250.87980.1177-0.4526-0.30660.2643-0.2850.01780.6094-0.4218-0.02190.4654-0.08020.03730.44080.05160.33520.8405-23.264927.4229
70.0947-0.0283-0.11240.0970.05950.22740.0101-0.405-0.024-0.56760.0821.61562.0971-0.4515-0.01280.6451-0.1732-0.00920.50680.04230.6467-6.7513-25.856211.5882
80.40070.12760.02380.5665-0.09830.20870.71161.68680.505-1.6023-0.67730.57880.83040.1581-0.00830.5442-0.00220.02610.5515-0.05490.5677-2.2121-20.42896.313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 55 )A17 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 75 )A56 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 103 )A76 - 103
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 120 )A104 - 120
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 508 )B2 - 508
7X-RAY DIFFRACTION7chain 'B' and (resid 509 through 514 )B509 - 514
8X-RAY DIFFRACTION8chain 'B' and (resid 515 through 519 )B515 - 519

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