[English] 日本語
Yorodumi- PDB-4pk7: crystal structure of human Stromal Antigen 2 (SA2) in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pk7 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | crystal structure of human Stromal Antigen 2 (SA2) in complex with Sister Chromatid Cohesion protein 1 (Scc1) with bound MES, native proteins | ||||||||||||
Components |
| ||||||||||||
Keywords | CELL CYCLE / Sister chromatid cohesion / cohesin subunits / protein-protein interaction / HEAT repeat | ||||||||||||
Function / homology | Function and homology information negative regulation of mitotic metaphase/anaphase transition / 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 / negative regulation of glial cell apoptotic process ...negative regulation of mitotic metaphase/anaphase transition / 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 / negative regulation of glial cell apoptotic process / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / 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 / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / meiotic cell cycle / condensed nuclear chromosome / chromosome segregation / fibrillar center / 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 / 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: 2.95 Å | ||||||||||||
Authors | Hara, K. / Chen, Z. / Tomchick, D.R. / Yu, H. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2014 Title: Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion. Authors: Hara, K. / Zheng, G. / Qu, Q. / Liu, H. / Ouyang, Z. / Chen, Z. / Tomchick, D.R. / Yu, H. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4pk7.cif.gz | 586.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4pk7.ent.gz | 491.5 KB | Display | PDB format |
PDBx/mmJSON format | 4pk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pk7_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4pk7_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 4pk7_validation.xml.gz | 34 KB | Display | |
Data in CIF | 4pk7_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pk/4pk7 ftp://data.pdbj.org/pub/pdb/validation_reports/pk/4pk7 | HTTPS FTP |
-Related structure data
Related structure data | 4pjuSC 4pjwC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 114980.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: STAG2, SA2 / Plasmid: pFastBac HT / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N3U4 |
---|---|
#2: Protein | Mass: 16772.426 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60216 |
#3: Chemical | ChemComp-MES / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.24 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.12 M Morpheus Divalents Mix, 0.1 M Morpheus Buffer System 1, and 27-30% (v/v) Morpheus EOD_P8K (Molecular Dimensions). |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2013 |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 32876 / Num. obs: 32876 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 1.8 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PJU Resolution: 2.95→47.677 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.65 / 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 mean: 88.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→47.677 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|