[English] 日本語
Yorodumi- PDB-5om0: CH2 chimera of human 14-3-3 sigma with the Gli1 phosphopeptide ar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5om0 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CH2 chimera of human 14-3-3 sigma with the Gli1 phosphopeptide around Ser640 | ||||||||||||
Components | 14-3-3 protein sigma,Zinc finger protein GLI1 | ||||||||||||
Keywords | SIGNALING PROTEIN / 14-3-3 proteins / Protein chimera / phosphopeptide-binding | ||||||||||||
Function / homology | Function and homology information notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / GLI-SUFU complex / regulation of hepatocyte proliferation / ventral midline development / epidermal cell differentiation / pituitary gland development / proximal/distal pattern formation / positive regulation of cell cycle G1/S phase transition / ciliary tip ...notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / GLI-SUFU complex / regulation of hepatocyte proliferation / ventral midline development / epidermal cell differentiation / pituitary gland development / proximal/distal pattern formation / positive regulation of cell cycle G1/S phase transition / ciliary tip / prostate gland development / cerebellar cortex morphogenesis / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / regulation of osteoblast differentiation / ciliary base / smoothened signaling pathway / digestive tract morphogenesis / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / spermatid development / axoneme / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Hedgehog 'off' state / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of cardiac muscle cell proliferation / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / positive regulation of DNA replication / stem cell proliferation / liver regeneration / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Degradation of GLI1 by the proteasome / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / Hedgehog 'on' state / negative regulation of protein kinase activity / negative regulation of canonical Wnt signaling pathway / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / osteoblast differentiation / response to wounding / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / positive regulation of cell growth / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / cadherin binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A. | ||||||||||||
Funding support | Russian Federation, United Kingdom, 3items
| ||||||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Chimeric 14-3-3 proteins for unraveling interactions with intrinsically disordered partners. Authors: Sluchanko, N.N. / Tugaeva, K.V. / Greive, S.J. / Antson, A.A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5om0.cif.gz | 365.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5om0.ent.gz | 306.8 KB | Display | PDB format |
PDBx/mmJSON format | 5om0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5om0 ftp://data.pdbj.org/pub/pdb/validation_reports/om/5om0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ok9C 5okfC 5omaC 5lu1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27810.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues 75-77 were mutated to Alanines to reduce surface entropy and improve crystallization. Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1, GLI1, GLI / Production host: Escherichia coli (E. coli) / References: UniProt: P31947, UniProt: P08151 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.51 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M bis-Tris (pH 6.5), 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→47 Å / Num. obs: 10910 / % possible obs: 99.6 % / Redundancy: 23 % / Biso Wilson estimate: 92.51 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 3.19→3.38 Å / Redundancy: 22.3 % / Rmerge(I) obs: 4.3 / Mean I/σ(I) obs: 0.91 / CC1/2: 0.5 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LU1 Resolution: 3.2→47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.497
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 240.94 Å2 / Biso mean: 141.58 Å2 / Biso min: 80.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.51 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.2→47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|