+Open data
-Basic information
Entry | Database: PDB / ID: 7ajk | ||||||
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Title | Crystal structure of CRYI-B Rac1 complex | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Actin / cytoskeleton / Rac1 / GTPase / Inhibitor | ||||||
Function / homology | Function and homology information MHC class Ib protein binding, via antigen binding groove / cellular response to molecule of bacterial origin / negative regulation of small GTPase mediated signal transduction / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / platelet degranulation / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis ...MHC class Ib protein binding, via antigen binding groove / cellular response to molecule of bacterial origin / negative regulation of small GTPase mediated signal transduction / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / platelet degranulation / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / negative regulation of actin filament polymerization / respiratory burst / WNT5:FZD7-mediated leishmania damping / regulation of chemotaxis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / regulation of establishment of cell polarity / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of memory T cell activation / positive regulation of Rho protein signal transduction / regulation of cell size / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / regulation of mitochondrial fission / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / Signal transduction by L1 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / platelet alpha granule lumen / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / ruffle membrane / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network Similarity search - Function | ||||||
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
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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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ajk.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ajk.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ajk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ajk_validation.pdf.gz | 724.8 KB | Display | wwPDB validaton report |
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Full document | 7ajk_full_validation.pdf.gz | 734.6 KB | Display | |
Data in XML | 7ajk_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 7ajk_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/7ajk ftp://data.pdbj.org/pub/pdb/validation_reports/aj/7ajk | HTTPS FTP |
-Related structure data
Related structure data | 7ajlC 4gzlS 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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Unit cell |
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-Components
#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 |
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#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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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 |
-Processing
Software |
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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
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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: 79.88 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→59.382 Å
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Refine LS restraints |
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LS refinement shell |
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