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- PDB-7xv0: Crystal structure of RPA70N-BLMp1 fusion -

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Basic information

Entry
Database: PDB / ID: 7xv0
TitleCrystal structure of RPA70N-BLMp1 fusion
Components
  • Bloom syndrome protein
  • Replication protein A 70 kDa DNA-binding subunit
KeywordsDNA BINDING PROTEIN / RPA / RPA70N / BLM
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / protein localization to chromosome / telomeric D-loop binding / DNA/DNA annealing activity / DNA replication factor A complex / telomere maintenance via semi-conservative replication / t-circle formation ...RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / protein localization to chromosome / telomeric D-loop binding / DNA/DNA annealing activity / DNA replication factor A complex / telomere maintenance via semi-conservative replication / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin / DNA geometric change / Y-form DNA binding / negative regulation of cell division / G-quadruplex DNA binding / cellular response to hydroxyurea / lateral element / bubble DNA binding / negative regulation of DNA recombination / DNA double-strand break processing / single-stranded telomeric DNA binding / chromatin-protein adaptor activity / Impaired BRCA2 binding to PALB2 / G-rich strand telomeric DNA binding / protein localization to site of double-strand break / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / regulation of cyclin-dependent protein serine/threonine kinase activity / 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) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / replication fork processing / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / PCNA-Dependent Long Patch Base Excision Repair / ATP-dependent activity, acting on DNA / Activation of the pre-replicative complex / response to X-ray / 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 / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / replication fork / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / cellular response to ionizing radiation / helicase activity / 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 / G2/M DNA damage checkpoint / base-excision repair / PML body / protein homooligomerization / Meiotic recombination / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Formation of Incision Complex in GG-NER / nuclear matrix / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / single-stranded DNA binding / site of double-strand break / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / 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
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / Replication factor-A protein 1, N-terminal domain / RQC domain / RQC / Replication factor A protein 1 ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) 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 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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 / 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 / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Bloom syndrome protein


Theoretical massNumber of molelcules
Total (without water)15,9862
Polymers15,9862
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-7 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.088, 53.644, 54.501
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 Replication protein A 70 kDa DNA-binding subunit / RP-A p70 / Replication factor A protein 1 / RF-A protein 1 / Single-stranded DNA-binding protein


Mass: 13663.812 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 Bloom syndrome protein / DNA helicase / RecQ-like type 2 / RecQ2 / RecQ protein-like 3


Mass: 2322.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P54132, DNA helicase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.74 Å3/Da / Density % sol: 29.37 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 2000 mM Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→38.23 Å / Num. obs: 33810 / % possible obs: 98.58 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.01362 / Net I/σ(I): 34.45
Reflection shellResolution: 1.5→1.554 Å / Rmerge(I) obs: 0.088 / Num. unique obs: 2484 / CC1/2: 0.996 / Rpim(I) all: 0.038

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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: 1.5→38.23 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1776 5.25 %
Rwork0.1687 32034 -
obs0.1704 33810 97.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.74 Å2 / Biso mean: 18.506 Å2 / Biso min: 7.98 Å2
Refinement stepCycle: final / Resolution: 1.5→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 0 125 1162
Biso mean---27.61 -
Num. residues----135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.25481060.182484259098
1.54-1.590.19421510.17612461261298
1.59-1.640.233990.17812519261899
1.64-1.70.2161310.17832477260899
1.7-1.760.26081610.18552451261299
1.76-1.840.24031470.19052483263099
1.84-1.940.15251350.17262507264299
1.94-2.060.21461380.16082443258198
2.06-2.220.19331430.16172466260998
2.22-2.450.18531580.16792436259497
2.45-2.80.19971150.17762475259098
2.8-3.530.20841790.172373255296
3.53-38.230.17841130.15522459257297
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)
14.2988-0.28630.94947.52310.2413.50350.09290.09160.0401-0.0879-0.09870.0895-0.00250.0728-0.00310.0429-0.00540.01410.0936-0.00860.0375.0524-6.4851-14.7276
21.7943-0.12960.53862.96831.10532.8697-0.0508-0.04940.2514-0.0057-0.05660.332-0.2879-0.21430.08780.1144-0.00680.01720.1060.00560.12741.0241-0.2084-3.3753
31.1578-0.1318-0.96520.8004-0.02792.21170.0193-0.0199-0.05170.0262-0.0230.057-0.0129-0.1230.00320.0899-0.0134-0.00850.1087-0.00390.10152.6224-2.78480.0657
40.0173-0.0924-0.05087.4205-1.64510.6811-0.0167-0.02760.02510.30480.04420.1646-0.08130.00070.00390.08950.0045-0.00570.12280.00120.0949-2.29453.3803-7.9849
51.8931-0.7508-0.25074.7539-1.2461.1045-0.0573-0.0924-0.14630.20020.06690.20910.0393-0.0303-0.02960.1043-0.0097-0.01160.1142-0.00250.0576-0.6826-6.3956-3.4297
63.0031-0.4524-0.59844.4415-1.82663.02120.1261-0.05140.339-0.1732-0.2278-0.4903-0.02650.19130.12760.0593-0.00720.01120.1110.01090.099412.5627-2.4621-10.9706
72.51450.083-1.68245.72430.75338.9033-0.3058-0.35810.72090.27220.1676-0.0002-0.40050.35870.06480.23860.0206-0.0470.1735-0.01260.1913.560112.28960.8675
83.1489-1.4349-0.42056.33942.39875.3803-0.1122-0.31770.21550.75120.00460.136-0.2337-0.07080.14920.34870.00650.03280.38390.03210.2911-4.279219.9402-0.6892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 15 )A0 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 40 )A16 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 75 )A41 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 91 )A76 - 91
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 108 )A92 - 108
6X-RAY DIFFRACTION6chain 'A' and (resid 109 through 121 )A109 - 121
7X-RAY DIFFRACTION7chain 'B' and (resid 147 through 154 )B147 - 154
8X-RAY DIFFRACTION8chain 'B' and (resid 155 through 160 )B155 - 160

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