|Entry||Database: PDB / ID: 6uzk|
|Title||Crystal Structure of the Ternary Complex of KRIT1 bound to both the Rap1 GTPase and HKi6|
|Keywords||CELL ADHESION / Complex / Small molecules / GTPase / KRIT1|
|Function / homology|
Function and homology information
negative regulation of synaptic vesicle exocytosis / Rap protein signal transduction / GTPase regulator activity / endothelium development / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / integrin activation / Rap1 signalling / establishment of endothelial barrier ...negative regulation of synaptic vesicle exocytosis / Rap protein signal transduction / GTPase regulator activity / endothelium development / regulation of cell junction assembly / negative regulation of calcium ion-dependent exocytosis / positive regulation of integrin activation / integrin activation / Rap1 signalling / establishment of endothelial barrier / regulation of establishment of cell polarity / MET activates RAP1 and RAC1 / azurophil granule membrane / negative regulation of endothelial cell migration / p130Cas linkage to MAPK signaling for integrins / small GTPase mediated signal transduction / negative regulation of endothelial cell proliferation / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of endothelial cell apoptotic process / regulation of angiogenesis / lipid droplet / G protein activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / negative regulation of angiogenesis / Integrin signaling / cell redox homeostasis / cellular response to cAMP / phosphatidylinositol-4,5-bisphosphate binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / GDP binding / Signaling by RAF1 mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by moderate kinase activity BRAF mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / cell population proliferation / microtubule binding / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cytoskeleton / GTPase activity / protein-containing complex binding / GTP binding / Neutrophil degranulation / extracellular space / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NUDIX, or N-terminal NPxY motif-rich, region of KRIT / KRIT, N-terminal NPxY motif-rich region / KRIT, N-terminal NPxY motif-rich domain superfamily / Krev interaction trapped protein 1, FERM domain C-lobe / Ras-related protein Rap1 / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / Small GTPase, Ras-type ...NUDIX, or N-terminal NPxY motif-rich, region of KRIT / KRIT, N-terminal NPxY motif-rich region / KRIT, N-terminal NPxY motif-rich domain superfamily / Krev interaction trapped protein 1, FERM domain C-lobe / Ras-related protein Rap1 / Ankyrin repeats (many copies) / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / Small GTPase, Ras-type / small GTPase Ras family profile. / FERM superfamily, second domain / FERM domain profile. / FERM domain / Band 4.1 homologues / Band 4.1 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras family / Small GTPase / Ankyrin repeat region circular profile. / Ankyrin repeat profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Krev interaction trapped protein 1 / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 2-hydroxy-6-methoxynaphthalene-1-carbaldehyde / Ras-related protein Rap-1b
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.924 Å|
|Funding support|| United States, 2items |
|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.J. / Sun, H. / Gongol, B. / Shyy, J.Y. / Ballatore, C. / Sklar, L.A. / Gingras, A.R.
|Structure viewer||Molecule: |
Downloads & links
A: Krev interaction trapped protein 1
B: Ras-related protein Rap-1b
-Protein , 2 types, 2 molecules A
|#1: Protein|| |
Mass: 37372.348 Da / Num. of mol.: 1
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
|#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 BL21(DE3) (bacteria) / References: UniProt: P61224
-Non-polymers , 4 types, 78 molecules
|#3: Chemical|| ChemComp-QMA / |
|#4: Chemical|| ChemComp-MG / |
|#5: Chemical|| ChemComp-GNP / |
|#6: Water|| ChemComp-HOH / |
|Has ligand of interest||Y|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 %|
|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|
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.999995 Å|
|Detector||Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2019|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.999995 Å / Relative weight: 1|
|Reflection||Resolution: 1.92→50 Å / Num. obs: 36147 / % possible obs: 94 % / Redundancy: 3 % / CC1/2: 0.991 / Net I/σ(I): 16.33|
|Reflection shell||Resolution: 1.92→1.95 Å / Num. unique obs: 1384 / CC1/2: 0.486|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4hdo
Resolution: 1.924→36.514 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.579 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.203 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å|
|Displacement parameters||Biso mean: 48.081 Å2|
|Refinement step||Cycle: LAST / Resolution: 1.924→36.514 Å|
|Refine LS restraints|
|LS refinement shell|
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