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Yorodumi- PDB-6oq3: Crystal Structure of the Ternary Complex of KRIT1 bound to both t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oq3 | ||||||
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Title | Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi2 | ||||||
Components |
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Keywords | CELL ADHESION / Complex / Small molecules / GTPase / KRIT1 | ||||||
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: 1.85 Å | ||||||
Authors | Gingras, A.R. | ||||||
Citation | Journal: Faseb Bioadv / Year: 2021 Title: Inhibition of the HEG1-KRIT1 interaction increases KLF4 and KLF2 expression in endothelial cells Authors: Lopez-Ramirez, M.A. / McCurdy, S. / Li, W. / Haynes, M.K. / Hale, P. / Francisco, K. / Oukoloff, K. / Bautista, M. / Choi, C.H. / Sun, H. / Gongol, B. / Shyy, J.Y. / Ballatore, C. / Sklar, L.A. / Gingras, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oq3.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oq3.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oq3 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oq3 | HTTPS FTP |
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-Related structure data
Related structure data | 6oq4C 4hdoS 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00522 |
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#2: Protein | Mass: 19020.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAP1B, OK/SW-cl.11 / Production host: Escherichia coli (E. coli) / References: UniProt: P61224 |
-Non-polymers , 4 types, 36 molecules
#3: Chemical | ChemComp-7WO / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GNP / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20-25% PEG 3,350, 100 mM Tris, pH 8.5, 100 mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→46.4 Å / Num. obs: 42373 / % possible obs: 98.6 % / Redundancy: 3.78 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.49 |
Reflection shell | Resolution: 1.85→1.96 Å / Rmerge(I) obs: 1.406 / Num. unique obs: 6656 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4hdo Resolution: 1.85→46.374 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.228 / SU B: 7.648 / SU ML: 0.202 / Average fsc free: 0.6882 / Average fsc work: 0.7082 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.173 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.232 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→46.374 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: 20
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