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Open data
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Basic information
Entry | Database: PDB / ID: 7xv0 | ||||||
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Title | Crystal structure of RPA70N-BLMp1 fusion | ||||||
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![]() | DNA BINDING PROTEIN / RPA / RPA70N / BLM | ||||||
Function / homology | ![]() 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 / 3'-5' DNA helicase activity / mitotic G2 DNA damage checkpoint signaling / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / telomere maintenance via telomerase / 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 / Fanconi Anemia Pathway / nucleotide-excision repair / 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 / protein homooligomerization / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, Y.Y. / Zang, N. / Fu, W.M. / Zhou, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.8 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.5 KB | Display | ![]() |
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Full document | ![]() | 429.8 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xutC ![]() 7xuvC ![]() 7xuwC ![]() 7xv1C ![]() 7xv4C ![]() 8jzvC ![]() 8jzyC ![]() 8k00C ![]() 5eayS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13663.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 2322.286 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.74 Å3/Da / Density % sol: 29.37 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 2000 mM Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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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: 50.74 Å2 / Biso mean: 18.506 Å2 / Biso min: 7.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→38.23 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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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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