+Open data
-Basic information
Entry | Database: PDB / ID: 1f3m | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE PAK1 | ||||||
Components | (SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA) x 2 | ||||||
Keywords | TRANSFERASE / Kinase domain / autoinhibitory fragment / homodimer | ||||||
Function / homology | Function and homology information negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / Activation of RAC1 / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of intracellular estrogen receptor signaling pathway / DSCAM interactions / RHOV GTPase cycle / regulation of axonogenesis / branching morphogenesis of an epithelial tube / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / stimulatory C-type lectin receptor signaling pathway / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / Sema3A PAK dependent Axon repulsion / Generation of second messenger molecules / intercalated disc / Smooth Muscle Contraction / RAC3 GTPase cycle / RAC2 GTPase cycle / ephrin receptor signaling pathway / localization / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of JUN kinase activity / positive regulation of stress fiber assembly / ruffle / RAC1 GTPase cycle / EPHB-mediated forward signaling / collagen binding / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / MAPK6/MAPK4 signaling / wound healing / G beta:gamma signalling through CDC42 / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cell-cell junction / cell migration / lamellipodium / positive regulation of peptidyl-serine phosphorylation / chromosome / actin cytoskeleton organization / nuclear membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of cell migration / intracellular signal transduction / chromatin remodeling / positive regulation of protein phosphorylation / axon / phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / dendrite / apoptotic process / DNA damage response / positive regulation of cell population proliferation / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Lei, M. / Lu, W. / Meng, W. / Parrini, M.-C. / Eck, M.J. / Mayer, B.J. / Harrison, S.C. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Structure of PAK1 in an autoinhibited conformation reveals a multistage activation switch. Authors: Lei, M. / Lu, W. / Meng, W. / Parrini, M.C. / Eck, M.J. / Mayer, B.J. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f3m.cif.gz | 164.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f3m.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 1f3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/1f3m ftp://data.pdbj.org/pub/pdb/validation_reports/f3/1f3m | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9180.215 Da / Num. of mol.: 2 / Fragment: PAK1 AUTOREGULATORY DOMAIN (70-149) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX2N / Production host: Escherichia coli (E. coli) References: UniProt: Q13153, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | Mass: 33273.234 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN (249-545) / Mutation: K299R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX2N / Production host: Escherichia coli (E. coli) References: UniProt: Q13153, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
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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: 3.88 Å3/Da / Density % sol: 68.33 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 12 ℃ / pH: 8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→34.08 Å / Num. all: 56156 / Num. obs: 56156 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.349 / % possible all: 97.4 |
Reflection | *PLUS Num. measured all: 160255 |
-Processing
Software |
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Refinement | Resolution: 2.3→34.08 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→34.08 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.237 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |