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- PDB-1f3m: CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE PAK1 -

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Basic information

Entry
Database: PDB / ID: 1f3m
TitleCRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE KINASE PAK1
Components(SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA) x 2
KeywordsTRANSFERASE / 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 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis ...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 / Ephrin signaling / CD28 dependent Vav1 pathway / regulation of axonogenesis / phosphorylation / RHOV GTPase cycle / branching morphogenesis of an epithelial tube / positive regulation of intracellular estrogen receptor signaling pathway / RHOJ GTPase cycle / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / exocytosis / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of MAPK cascade / RHOU GTPase cycle / CDC42 GTPase cycle / RHOH GTPase cycle / Generation of second messenger molecules / positive regulation of JUN kinase activity / Sema3A PAK dependent Axon repulsion / intercalated disc / ephrin receptor signaling pathway / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate PKNs / positive regulation of peptidyl-serine phosphorylation / collagen binding / positive regulation of stress fiber assembly / ruffle / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / CD209 (DC-SIGN) signaling / neuron projection morphogenesis / cellular response to starvation / Signal transduction by L1 / VEGFR2 mediated vascular permeability / actin filament / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / Z disc / ruffle membrane / G beta:gamma signalling through CDC42 / cell-cell junction / cell migration / lamellipodium / positive regulation of protein phosphorylation / chromosome / actin cytoskeleton organization / protein autophosphorylation / nuclear membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / protein phosphorylation / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / centrosome / dendrite / DNA damage response / protein-containing complex / nucleoplasm / ATP binding
Similarity search - Function
SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 ...SerineThreonine-protein kinase PAK-alpha; Chain A / CRIB domain / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsLei, M. / Lu, W. / Meng, W. / Parrini, M.-C. / Eck, M.J. / Mayer, B.J. / Harrison, S.C.
CitationJournal: 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
DepositionJun 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA
C: SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA
B: SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA
D: SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46032
Polymers84,9074
Non-polymers3,55328
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-55 kcal/mol
Surface area33850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.583, 94.583, 147.497
Angle α, β, γ (deg.)90, 90, 90
Int Tables number76
Space group name H-MP41

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA


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 SERINE/THREONINE-PROTEIN KINASE PAK-ALPHA


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 / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.8-1.9 Mammonium sulfate1reservoir
2150 mM1reservoirNaCl
3250-300 mM1reservoirNaI
410 mMdithiothreitol1reservoir
5100 mMPIPES1reservoir
6125 mM1dropNaCl
720 mMTris-HCl1drop
8protein1drop15-20mg

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.3→2.37 Å / Redundancy: 3 % / Rmerge(I) obs: 0.349 / % possible all: 97.4
Reflection
*PLUS
Num. measured all: 160255

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.3→34.08 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.258 2848 -
Rwork0.237 --
all0.237 56156 -
obs0.258 56156 92.6 %
Refinement stepCycle: LAST / Resolution: 2.3→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5577 0 28 582 6187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.32
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

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