+Open data
-Basic information
Entry | Database: PDB / ID: 7xv4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of RPA70N-ATRIP fusion | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN / RPA / RPA70N / ATRIP | ||||||
Function / homology | Function and homology information ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / regulation of double-strand break repair / 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) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...ATR-ATRIP complex / protein localization to chromosome / DNA replication factor A complex / chromatin-protein adaptor activity / regulation of double-strand break repair / 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) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / nucleobase-containing compound metabolic process / K63-linked polyubiquitin modification-dependent protein binding / 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 / 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 / DNA damage checkpoint signaling / 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 / 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 / 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 / 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
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xv4.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xv4.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 7xv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xv4 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xv4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7xutC 7xuvC 7xuwC 7xv0C 7xv1C 8jzvC 8jzyC 8k00C 5eayS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13274.449 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 | Mass: 1839.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATRIP, AGS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXE1 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.82 % |
---|---|
Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2400 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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→38.28 Å / Num. obs: 29274 / % possible obs: 99.97 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.03727 / Rpim(I) all: 0.01094 / Net I/σ(I): 43.83 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 0.149 / Num. unique obs: 2826 / CC1/2: 0.995 / Rpim(I) all: 0.04257 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EAY Resolution: 1.6→38.28 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.94 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.68 Å2 / Biso mean: 22.5865 Å2 / Biso min: 9.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→38.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|