+Open data
-Basic information
Entry | Database: PDB / ID: 7xuv | ||||||
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Title | Crystal structure of RPA70N-RMI1 fusion | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / RPA / RPA70N / RMI1 | ||||||
Function / homology | Function and homology information reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / resolution of meiotic recombination intermediates / protein localization to site of double-strand break / single-stranded telomeric DNA binding / Removal of the Flap Intermediate ...reduction of food intake in response to dietary excess / RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / resolution of meiotic recombination intermediates / protein localization to site of double-strand break / single-stranded telomeric DNA binding / Removal of the Flap Intermediate / 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 / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / site of DNA damage / Presynaptic phase of homologous DNA pairing and strand exchange / 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 / mismatch repair / response to glucose / 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 / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / meiotic cell cycle / nucleotide-excision repair / Fanconi Anemia Pathway / Recognition of DNA damage by PCNA-containing replication complex / 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 / multicellular organism growth / Dual Incision in GG-NER / DNA-templated DNA replication / PML body / Meiotic recombination / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / glucose homeostasis / site of double-strand break / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / nucleotide binding / DNA repair / DNA damage response / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 | 7xuv.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xuv.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 7xuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/7xuv ftp://data.pdbj.org/pub/pdb/validation_reports/xu/7xuv | HTTPS FTP |
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-Related structure data
Related structure data | 7xutC 7xuwC 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: 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 |
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#2: Protein/peptide | Mass: 2351.306 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RMI1, C9orf76 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A7 |
#3: 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: 1.73 Å3/Da / Density % sol: 28.96 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 30% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→36.24 Å / Num. obs: 22637 / % possible obs: 89.41 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.0317 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 0.342 / Num. unique obs: 2779 / CC1/2: 0.953 / Rpim(I) all: 0.1578 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EAY Resolution: 1.6→36.24 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.18 / 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: 47.82 Å2 / Biso mean: 21.2182 Å2 / Biso min: 9.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→36.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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