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Yorodumi- PDB-3rqe: Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rqe | ||||||
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Title | Cerebral cavernous malformation 3 (CCM3) in complex with paxillin LD1 | ||||||
Components |
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Keywords | PROTEIN BINDING / Protein-peptide complex / FAT domain / Dimerization / Cerebral Cavernous Malformation | ||||||
Function / homology | Function and homology information FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / 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 / negative regulation of cell migration involved in sprouting angiogenesis ...FAR/SIN/STRIPAK complex / intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of Golgi organization / 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 / negative regulation of cell migration involved in sprouting angiogenesis / wound healing, spreading of cells / stress-activated protein kinase signaling cascade / positive regulation of Notch signaling pathway / regulation of angiogenesis / cellular response to leukemia inhibitory factor / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / angiogenesis / protein stabilization / positive regulation of cell migration / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / protein homodimerization activity / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Homo Sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Li, X. / Zhang, R. / Boggon, T.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Molecular Recognition of Leucine-Aspartate Repeat (LD) Motifs by the Focal Adhesion Targeting Homology Domain of Cerebral Cavernous Malformation 3 (CCM3). Authors: Li, X. / Ji, W. / Zhang, R. / Folta-Stogniew, E. / Min, W. / Boggon, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rqe.cif.gz | 320.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rqe.ent.gz | 267.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/3rqe ftp://data.pdbj.org/pub/pdb/validation_reports/rq/3rqe | HTTPS FTP |
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-Related structure data
Related structure data | 3rqfC 3rqgC 3l8iS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 24930.779 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD10 / Plasmid: modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9BUL8 #2: Protein/peptide | | Mass: 1491.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo Sapiens (human) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1-0.2 M potassium fluoride, 15-20% PEG3350., pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010 / Details: mirrors |
Radiation | Monochromator: horizontally focusing Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 81.5 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.86 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3L8I Resolution: 2.8→38.92 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.893 / SU B: 37.203 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.45 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.056 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→38.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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