[English] 日本語
Yorodumi- PDB-7lin: X-ray structure of SPOP MATH domain (D140G) in complex with a 53B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lin | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide | ||||||||||||
Components |
| ||||||||||||
Keywords | PROTEIN BINDING / SPOP / 53BP1 / DNA damage response / Homologous recombination / Ubiquitin ligase | ||||||||||||
Function / homology | Function and homology information ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / regulation of proteolysis / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / telomeric DNA binding ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / regulation of proteolysis / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / DNA repair complex / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / telomeric DNA binding / SUMOylation of transcription factors / negative regulation of double-strand break repair via homologous recombination / histone reader activity / methylated histone binding / DNA damage checkpoint signaling / replication fork / Nonhomologous End-Joining (NHEJ) / transcription coregulator activity / Hedgehog 'on' state / protein homooligomerization / G2/M DNA damage checkpoint / kinetochore / positive regulation of DNA-binding transcription factor activity / double-strand break repair via nonhomologous end joining / protein polyubiquitination / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / nuclear body / nuclear speck / ubiquitin protein ligase binding / DNA damage response / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||||||||
Authors | Botuyan, M.V. / Cui, G. / Mer, G. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Sci Adv / Year: 2021 Title: ATM-phosphorylated SPOP contributes to 53BP1 exclusion from chromatin during DNA replication. Authors: Wang, D. / Ma, J. / Botuyan, M.V. / Cui, G. / Yan, Y. / Ding, D. / Zhou, Y. / Krueger, E.W. / Pei, J. / Wu, X. / Wang, L. / Pei, H. / McNiven, M.A. / Ye, D. / Mer, G. / Huang, H. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7lin.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7lin.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 7lin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/7lin ftp://data.pdbj.org/pub/pdb/validation_reports/li/7lin | HTTPS FTP |
---|
-Related structure data
Related structure data | 7lioC 7lipC 7liqC 3hqmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16434.949 Da / Num. of mol.: 1 / Fragment: MATH domain / Mutation: D140G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791 |
---|---|
#2: Protein/peptide | Mass: 1392.423 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12888 |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.28 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, ...Details: SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio. Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→24.32 Å / Num. obs: 33113 / % possible obs: 98.21 % / Redundancy: 8.1 % / Biso Wilson estimate: 14.36 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.012 / Rrim(I) all: 0.034 / Net I/σ(I): 43.35 |
Reflection shell | Resolution: 1.44→1.49 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.15 / Num. unique obs: 3207 / CC1/2: 0.985 / CC star: 0.996 / Rpim(I) all: 0.06 / Rrim(I) all: 0.17 / % possible all: 97.15 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HQM Resolution: 1.44→24.32 Å / SU ML: 0.0895 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.28 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→24.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|