|Entry||Database: PDB / ID: 7ajk|
|Title||Crystal structure of CRYI-B Rac1 complex|
|Keywords||CYTOSOLIC PROTEIN / Actin / cytoskeleton / Rac1 / GTPase / Inhibitor|
|Function / homology|
Function and homology information
MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / cellular response to molecule of bacterial origin / platelet degranulation / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex ...MHC class Ib protein binding, via antigen binding groove / negative regulation of small GTPase mediated signal transduction / cellular response to molecule of bacterial origin / platelet degranulation / regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / Rho GDP-dissociation inhibitor binding / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / negative regulation of actin filament polymerization / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of chemotaxis / PCP/CE pathway / cell projection assembly / RHO GTPases activate CIT / RHO GTPases activate KTN1 / cortical cytoskeleton organization / ruffle organization / hepatocyte growth factor receptor signaling pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / Azathioprine ADME / regulation of stress fiber assembly / negative regulation of fibroblast migration / sphingosine-1-phosphate receptor signaling pathway / thioesterase binding / Wnt signaling pathway, planar cell polarity pathway / regulation of mitochondrial fission / regulation of lamellipodium assembly / Nef and signal transduction / motor neuron axon guidance / Sema4D mediated inhibition of cell attachment and migration / Activation of RAC1 / positive regulation of Rho protein signal transduction / regulation of establishment of cell polarity / positive regulation of cell-substrate adhesion / Ephrin signaling / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / CD28 dependent Vav1 pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / semaphorin-plexin signaling pathway / NRAGE signals death through JNK / regulation of cell size / positive regulation of memory T cell activation / Rac protein signal transduction / DSCAM interactions / positive regulation of lamellipodium assembly / establishment or maintenance of cell polarity / small GTPase mediated signal transduction / RHO GTPases activate PAKs / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate NADPH Oxidases / RHO GTPases activate PKNs / localization / regulation of actin cytoskeleton organization / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of microtubule polymerization / G protein activity / positive regulation of stress fiber assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / RAC1 GTPase cycle / neuron migration / actin filament polymerization / small monomeric GTPase / cell-matrix adhesion / substrate adhesion-dependent cell spreading / cell motility / actin filament organization / secretory granule membrane / RHO GTPases Activate Formins / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of endothelial cell migration / platelet alpha granule lumen / Signal transduction by L1 / cell projection / cilium / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling
Similarity search - Function
CYFIP-related Rac1 interactor / CYRIA/CYRIB, Rac1 binding domain / CYRIA/CYRIB Rac1 binding domain / small GTPase Rho family profile. / Small GTPase Rho / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1 / CYFIP-related Rac1 interactor B
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å|
|Authors||Yelland, T. / Anh, L. / Insall, R. / Machesky, L. / Ismail, S.|
|Funding support||1items |
|Citation||Journal: Structure / Year: 2021|
Title: Structural Basis of CYRI-B Direct Competition with Scar/WAVE Complex for Rac1.
Authors: Yelland, T. / Le, A.H. / Nikolaou, S. / Insall, R. / Machesky, L. / Ismail, S.
|Structure viewer||Molecule: |
Downloads & links
BBB: Ras-related C3 botulinum toxin substrate 1
CCC: CYFIP-related Rac1 interactor B
|#1: Protein|| |
Mass: 19836.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Production host: Escherichia coli (E. coli) / References: UniProt: P63000, small monomeric GTPase
|#2: Protein|| |
Mass: 36848.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CYRIB, CYRI, FAM49B, BM-009 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NUQ9
|#3: Chemical|| ChemComp-MG / |
|#4: Chemical|| ChemComp-GNP / |
|#5: Water|| ChemComp-HOH / |
|Has ligand of interest||Y|
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 %|
|Crystal grow||Temperature: 279 K / Method: vapor diffusion, sitting drop|
Details: 8% v/v PEG4,000 0.1M Tris pH 8.5 0.2M Sodium acetate
|Diffraction||Mean temperature: 100 K / Serial crystal experiment: N|
|Diffraction source||Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å|
|Detector||Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2020|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97624 Å / Relative weight: 1|
|Reflection||Resolution: 3.1→59.382 Å / Num. obs: 13493 / % possible obs: 97.92 % / Redundancy: 10.6 % / CC1/2: 0.99 / Net I/σ(I): 18.7|
|Reflection shell||Resolution: 3.1→3.21 Å / Num. unique obs: 2398 / CC1/2: 0.917|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 4GZL
Resolution: 3.1→59.382 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.891 / SU B: 23.055 / SU ML: 0.397 / Cross valid method: FREE R-VALUE / ESU R Free: 0.475
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 / Solvent model: MASK BULK SOLVENT|
|Displacement parameters||Biso mean: 79.88 Å2|
|Refinement step||Cycle: LAST / Resolution: 3.1→59.382 Å|
|Refine LS restraints|
|LS refinement shell|
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