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Yorodumi- PDB-4hdo: Crystal structure of the binary Complex of KRIT1 bound to the Rap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hdo | ||||||
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Title | Crystal structure of the binary Complex of KRIT1 bound to the Rap1 GTPase | ||||||
Components |
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Keywords | SIGNALING PROTEIN / RA binding motif / PTB fold / GTPase / GTP / Rap effector / Rap1 / HEG1 / Cell-cell junctions / nucleus | ||||||
Function / homology | Function and homology information Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation ...Rap protein signal transduction / modification of postsynaptic structure / GTPase regulator activity / regulation of cell junction assembly / endothelium development / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / negative regulation of synaptic vesicle exocytosis / calcium-ion regulated exocytosis / integrin activation / Rap1 signalling / negative regulation of endothelial cell migration / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / p130Cas linkage to MAPK signaling for integrins / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / cellular response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / Integrin signaling / negative regulation of angiogenesis / cell redox homeostasis / small monomeric GTPase / G protein activity / establishment of localization in cell / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / microtubule binding / angiogenesis / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / GTPase activity / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / GTP binding / protein-containing complex / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Gingras, A.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The Structure of the Ternary Complex of Krev Interaction Trapped 1 (KRIT1) Bound to Both the Rap1 GTPase and the Heart of Glass (HEG1) Cytoplasmic Tail. Authors: Gingras, A.R. / Puzon-McLaughlin, W. / Ginsberg, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hdo.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hdo.ent.gz | 88.1 KB | Display | PDB format |
PDBx/mmJSON format | 4hdo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/4hdo ftp://data.pdbj.org/pub/pdb/validation_reports/hd/4hdo | HTTPS FTP |
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-Related structure data
Related structure data | 4hdqC 1c1yS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37372.348 Da / Num. of mol.: 1 / Fragment: FERM domain (UNP residues 417-736) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pLEICS-07 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: O00522 |
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#2: Protein | Mass: 19020.508 Da / Num. of mol.: 1 / Fragment: UNP residues 1-167 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Plasmid: pTAC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P61224 |
-Non-polymers , 4 types, 271 molecules
#3: Chemical | ChemComp-GOL / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GNP / |
#6: 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: 2.35 Å3/Da / Density % sol: 47.58 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15% PEG2000 MME, 100 mM Tris, 100 mM potassium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 57913 / Num. obs: 57913 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 31.27 |
Reflection shell | Resolution: 1.67→1.77 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.37 / Num. unique all: 21549 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C1Y Resolution: 1.67→32.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.1 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→32.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.715 Å / Total num. of bins used: 20
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