+Open data
-Basic information
Entry | Database: PDB / ID: 2c2h | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP | ||||||
Components | RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 | ||||||
Keywords | SIGNALING PROTEIN / GTPASE RAC3 / SMALL GTP BINDING PROTEIN / P21 RAC / RAS- RELATED C3 BUTULINUM TOXIN SUBSTRATE 3 | ||||||
Function / homology | Function and homology information cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / cell projection assembly / synaptic transmission, GABAergic ...cerebral cortex GABAergic interneuron development / regulation of neuron maturation / regulation of neutrophil migration / postsynaptic actin cytoskeleton organization / engulfment of apoptotic cell / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / cell projection assembly / synaptic transmission, GABAergic / motor neuron axon guidance / PCP/CE pathway / positive regulation of cell adhesion mediated by integrin / establishment or maintenance of cell polarity / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / RAC3 GTPase cycle / endomembrane system / positive regulation of substrate adhesion-dependent cell spreading / homeostasis of number of cells within a tissue / cell chemotaxis / small monomeric GTPase / G protein activity / actin filament organization / cell periphery / regulation of actin cytoskeleton organization / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / growth cone / actin cytoskeleton organization / cytoplasmic vesicle / cytoskeleton / intracellular signal transduction / neuron projection / GTPase activity / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / GTP binding / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. ...Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Human Rac3 in Complex with Gdp Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / ...Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c2h.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c2h.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 2c2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c2h_validation.pdf.gz | 3.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2c2h_full_validation.pdf.gz | 3.9 MB | Display | |
Data in XML | 2c2h_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2c2h_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c2h ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c2h | HTTPS FTP |
-Related structure data
Related structure data | 1g4uS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 177 / Label seq-ID: 3 - 177
NCS oper: (Code: given Matrix: (0.16319, 0.9865, 0.0136), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21359.770 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60763 |
---|
-Non-polymers , 5 types, 196 molecules
#2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | ENGINEERED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.6 % |
---|---|
Crystal grow | pH: 7.5 Details: 30% MPD, 0.5 M AMMONIUM SULFATE, 0.1 M HEPES PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0038 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0038 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→27.07 Å / Num. obs: 28734 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 93.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G4U Resolution: 1.85→62.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.301 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.62 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→62.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|