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Yorodumi- PDB-3w8i: Crystal structure of CCM3 in complex with the C-terminal regulato... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w8i | ||||||
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Title | Crystal structure of CCM3 in complex with the C-terminal regulatory domain of MST4 | ||||||
Components |
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Keywords | PROTEIN BINDING/TRANSFERASE / PROTEIN BINDING-TRANSFERASE complex | ||||||
Function / homology | Function and homology information FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / microvillus assembly / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / Golgi reassembly / positive regulation of stress-activated MAPK cascade / endothelium development / establishment of Golgi localization / positive regulation of intracellular protein transport / vesicle membrane / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / Golgi-associated vesicle / positive regulation of Notch signaling pathway / Apoptotic cleavage of cellular proteins / regulation of angiogenesis / cellular response to starvation / negative regulation of cell migration / cellular response to leukemia inhibitory factor / cell periphery / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / regulation of apoptotic process / angiogenesis / protein autophosphorylation / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / apical plasma membrane / Golgi membrane / protein phosphorylation / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / magnesium ion binding / protein homodimerization activity / extracellular exosome / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Xu, X. / Wang, D.C. / Ding, J. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structural Basis for the Unique Heterodimeric Assembly between Cerebral Cavernous Malformation 3 and Germinal Center Kinase III. Authors: Xu, X. / Wang, X. / Zhang, Y. / Wang, D.C. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w8i.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w8i.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 3w8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/3w8i ftp://data.pdbj.org/pub/pdb/validation_reports/w8/3w8i | HTTPS FTP |
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-Related structure data
Related structure data | 3w8hC 3ajmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24896.619 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 8-212 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCM3, PDCD10, TFAR15 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BUL8 |
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#2: Protein | Mass: 8205.410 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 346-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MASK, MST4, SOK1, STK25, YSK1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9P289, non-specific serine/threonine protein kinase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.1M Bis-Tris, 25% PEG3350, 0.3M ammonium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.85 Å / Num. all: 11764 / Num. obs: 11764 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1666 / Rsym value: 0.353 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AJM Resolution: 2.4→45.12 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 26.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.618 Å2 / ksol: 0.328 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.12 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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