+Open data
-Basic information
Entry | Database: PDB / ID: 7zjs | |||||||||
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Title | Structural basis of centromeric cohesion protection by SGO1 | |||||||||
Components |
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Keywords | CELL CYCLE / cohesin / STAG2 / SGO1 / HEAT | |||||||||
Function / homology | Function and homology information mitotic sister chromatid cohesion, centromeric / negative regulation of mitotic metaphase/anaphase transition / centriole-centriole cohesion / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex ...mitotic sister chromatid cohesion, centromeric / negative regulation of mitotic metaphase/anaphase transition / centriole-centriole cohesion / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / meiotic chromosome segregation / negative regulation of glial cell apoptotic process / attachment of spindle microtubules to kinetochore / meiotic sister chromatid cohesion / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / condensed chromosome, centromeric region / chromatin looping / reciprocal meiotic recombination / lncRNA binding / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic spindle pole / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / RHO GTPases Activate Formins / kinetochore / fibrillar center / kinase binding / nuclear matrix / spindle pole / Separation of Sister Chromatids / double-strand break repair / chromosome / midbody / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / cell division / centrosome / apoptotic process / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å | |||||||||
Authors | Patel, A. / Panne, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2023 Title: Structural basis of centromeric cohesion protection. Authors: Garcia-Nieto, A. / Patel, A. / Li, Y. / Oldenkamp, R. / Feletto, L. / Graham, J.J. / Willems, L. / Muir, K.W. / Panne, D. / Rowland, B.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zjs.cif.gz | 794.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zjs.ent.gz | 634.7 KB | Display | PDB format |
PDBx/mmJSON format | 7zjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zjs_validation.pdf.gz | 489.2 KB | Display | wwPDB validaton report |
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Full document | 7zjs_full_validation.pdf.gz | 517.6 KB | Display | |
Data in XML | 7zjs_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 7zjs_validation.cif.gz | 89.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/7zjs ftp://data.pdbj.org/pub/pdb/validation_reports/zj/7zjs | HTTPS FTP |
-Related structure data
Related structure data | 6qnxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 141502.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAG2, SA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3U4 #2: Protein | Mass: 71772.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1, SCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60216 #3: Protein/peptide | Mass: 1315.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5FBB7 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.06 M Morpheus Divalents mix, 0.1 M Morpheus buffer system 2, 48% (v/v) Morpheus EOD_P8K |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.24→47.87 Å / Num. obs: 48451 / % possible obs: 99.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 108.36 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.24→3.35 Å / Num. unique obs: 4517 / CC1/2: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QNX Resolution: 3.24→47.87 Å / SU ML: 0.5833 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4685 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 129.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.24→47.87 Å
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Refine LS restraints |
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LS refinement shell |
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