+Open data
-Basic information
Entry | Database: PDB / ID: 7xuw | ||||||
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Title | Crystal structure of RPA70N-BLMp2 fusion | ||||||
Components | fusion protein of Replication protein A 70 kDa DNA-binding subunit and Bloom syndrome protein | ||||||
Keywords | DNA BINDING PROTEIN / RPA / RPA70N / BLM | ||||||
Function / homology | Function and homology information regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / protein localization to chromosome / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication ...regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / protein localization to chromosome / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication / DNA replication factor A complex / cellular response to camptothecin / t-circle formation / G-quadruplex DNA unwinding / telomeric D-loop disassembly / Y-form DNA binding / chromatin-protein adaptor activity / negative regulation of cell division / four-way junction helicase activity / G-quadruplex DNA binding / DNA double-strand break processing / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / bubble DNA binding / Removal of the Flap Intermediate / single-stranded telomeric DNA binding / Processive synthesis on the C-strand of the telomere / protein localization to site of double-strand break / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Impaired BRCA2 binding to PALB2 / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / DNA 3'-5' helicase / replisome / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / regulation of cyclin-dependent protein serine/threonine kinase activity / nuclear chromosome / replication fork processing / DNA unwinding involved in DNA replication / mitotic G2 DNA damage checkpoint signaling / 3'-5' DNA helicase activity / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / telomere maintenance via telomerase / response to X-ray / Activation of the pre-replicative complex / PCNA-Dependent Long Patch Base Excision Repair / Regulation of HSF1-mediated heat shock response / HSF1 activation / ATP-dependent activity, acting on DNA / mismatch repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / isomerase activity / telomere maintenance / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / helicase activity / meiotic cell cycle / replication fork / molecular function activator activity / cellular response to ionizing radiation / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / double-strand break repair via homologous recombination / base-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / protein homooligomerization / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / nuclear matrix / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / protein complex oligomerization / chromosome / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wu, Y.Y. / Zang, N. / Fu, W.M. / Zhou, C. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xuw.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xuw.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 7xuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xuw_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 7xuw_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 7xuw_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 7xuw_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/7xuw ftp://data.pdbj.org/pub/pdb/validation_reports/xu/7xuw | HTTPS FTP |
-Related structure data
Related structure data | 7xutC 7xuvC 7xv0C 7xv1C 7xv4C 8jzvC 8jzyC 8k00C 5eayS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.39 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.93 Å2 / Biso mean: 26.7718 Å2 / Biso min: 11.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→27.94 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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