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- PDB-7xuw: Crystal structure of RPA70N-BLMp2 fusion -

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Basic information

Entry
Database: PDB / ID: 7xuw
TitleCrystal structure of RPA70N-BLMp2 fusion
Componentsfusion protein of Replication protein A 70 kDa DNA-binding subunit and Bloom syndrome protein
KeywordsDNA BINDING PROTEIN / RPA / RPA70N / BLM
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / protein localization to chromosome / telomeric G-quadruplex DNA binding / DNA/DNA annealing activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA replication factor A complex / telomere maintenance via semi-conservative replication ...RecQ family helicase-topoisomerase III complex / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / protein localization to chromosome / telomeric G-quadruplex DNA binding / DNA/DNA annealing activity / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA replication factor A complex / telomere maintenance via semi-conservative replication / t-circle formation / telomeric D-loop disassembly / DNA geometric change / cellular response to camptothecin / Y-form DNA binding / negative regulation of cell division / cellular response to hydroxyurea / four-way junction helicase activity / G-quadruplex DNA binding / bubble DNA binding / DNA double-strand break processing / negative regulation of DNA recombination / lateral element / Impaired BRCA2 binding to PALB2 / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / Removal of the Flap Intermediate / chromatin-protein adaptor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / protein localization to site of double-strand break / Processive synthesis on the C-strand of the telomere / 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 / 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 / HDR through Single Strand Annealing (SSA) / DNA 3'-5' helicase / nuclear chromosome / 3'-5' DNA helicase activity / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / replication fork processing / hemopoiesis / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / Activation of the pre-replicative complex / response to X-ray / ATP-dependent activity, acting on DNA / HSF1 activation / telomere maintenance via telomerase / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / homeostasis of number of cells within a tissue / telomere maintenance / DNA helicase activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / cellular response to ionizing radiation / meiotic cell cycle / male germ cell nucleus / nucleotide-excision repair / Fanconi Anemia Pathway / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / helicase activity / double-strand break repair via homologous recombination / base-excision repair / PML body / G2/M DNA damage checkpoint / protein homooligomerization / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / Meiotic recombination / 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 / in utero embryonic development
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 / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain ...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 / Replication factor A protein 1 / Replication factor-A protein 1, N-terminal / Replication protein A, OB domain / Replication protein A OB domain / RQC domain / RQC / RQC domain / : / Replication factor A, C-terminal / Replication factor-A C terminal domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain / DNA helicase, ATP-dependent, RecQ type / HRDC domain profile. / 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: 1.8 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: fusion protein of Replication protein A 70 kDa DNA-binding subunit and Bloom syndrome protein


Theoretical massNumber of molelcules
Total (without water)16,1561
Polymers16,1561
Non-polymers00
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.476, 62.476, 69.497
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 fusion protein of Replication protein A 70 kDa DNA-binding subunit and Bloom syndrome protein / 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 2 / RecQ2 / RecQ protein-like 3


Mass: 16156.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fusion protein(3-121:RPA70N(P27694), 122-125:linker, 550-564:BLMp2(P54132))
Source: (gene. exp.) Homo sapiens (human) / Gene: RPA1, REPA1, RPA70, BLM, RECQ2, RECQL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P27694, UniProt: P54132, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 8% PEG 4000

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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→27.94 Å / Num. obs: 24353 / % possible obs: 99.92 % / Redundancy: 12.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1312 / Rpim(I) all: 0.03932 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.7671 / Num. unique obs: 2918 / CC1/2: 0.954 / Rpim(I) all: 0.2215 / % 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→27.94 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1163 4.78 %
Rwork0.1928 23190 -
obs0.1941 24353 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.93 Å2 / Biso mean: 26.7718 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 1.8→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 0 94 1153
Biso mean---32.03 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.880.28131320.231129183050
1.88-1.980.21481370.209329023039
1.98-2.110.27641440.202929043048
2.11-2.270.19331320.180829083040
2.27-2.50.21841580.206728973055
2.5-2.860.25051680.209628643032
2.86-3.60.21681400.204529073047
3.6-27.940.19011520.167528903042
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)
12.9258-0.25670.64484.6995-0.39973.82990.1598-0.10040.0038-0.2541-0.02460.38230.2344-0.1092-0.15290.1608-0.0341-0.0310.2153-0.00590.2215-23.6587-6.9871-14.4105
23.4562-0.6028-1.84643.9313-2.80264.403-0.3153-0.449-2.10120.23650.20820.85681.3466-0.4198-0.06830.3668-0.0841-0.03030.31030.06580.5592-21.5881-14.7209-18.9172
34.4955-2.38310.4342.6552-1.19271.0745-0.212-0.31290.28160.12110.0391-0.71170.09290.15690.08190.1316-0.03960.00160.20410.03140.197-9.7151-2.0089-13.833
44.6119-2.65-1.5323.20180.58841.882-0.167-0.1070.56980.2222-0.0838-0.77970.35550.62270.11520.16360.0476-0.01090.26830.05290.2575-1.4121-8.2282-10.3062
52.52930.4953-0.81752.2015-0.19623.3992-0.22610.2327-0.1709-0.05130.0339-0.2660.22920.20920.20880.1395-0.03560.00380.17260.01030.1609-8.9599-7.8997-15.1588
66.4974-0.98160.38811.4907-1.39651.26240.2973-0.0022-0.1332-0.4184-0.0864-0.7779-0.38141.11890.09160.3233-0.08950.02860.43220.07240.4672-4.82-0.418-21.0312
71.6845-0.07790.99421.166-0.77943.50930.0730.2188-0.0502-0.1660.00680.01630.29420.3469-0.00310.13630.00180.01650.1429-0.01990.1621-13.5014-14.719-12.7026
81.3507-1.29330.19562.74770.1984.48430.0050.11790.2329-0.3459-0.0144-0.1368-0.44260.05460.0050.1386-0.0728-0.0110.1374-0.01660.181-15.8462-2.5963-14.5364
93.2187-2.27862.83074.0323-1.4432.4098-0.1838-0.3162-0.35190.51320.210.4099-0.4819-0.43530.04480.29510.04530.01450.2644-0.00920.2588-19.2111-2.70024.3432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 16 )A4 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 23 )A17 - 23
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 32 )A24 - 32
4X-RAY DIFFRACTION4chain 'A' and (resid 33 through 47 )A33 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 67 )A48 - 67
6X-RAY DIFFRACTION6chain 'A' and (resid 68 through 75 )A68 - 75
7X-RAY DIFFRACTION7chain 'A' and (resid 76 through 91 )A76 - 91
8X-RAY DIFFRACTION8chain 'A' and (resid 92 through 125 )A92 - 125
9X-RAY DIFFRACTION9chain 'A' and (resid 550 through 564 )A550 - 564

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