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- PDB-3dvp: Pak1 peptide bound LC8 -

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Basic information

Entry
Database: PDB / ID: 3dvp
TitlePak1 peptide bound LC8
Components
  • Dynein light chain 1, cytoplasmic
  • P21 activated Kinase peptide
KeywordsSTRUCTURAL PROTEIN / MOTOR PROTEIN / Pak1 / LC8 / DLC1 / PIN / Complex / Dynein / Microtubule
Function / homology
Function and homology information


spermatid nucleus elongation / positive regulation of neuron remodeling / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / negative regulation of cell proliferation involved in contact inhibition ...spermatid nucleus elongation / positive regulation of neuron remodeling / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / negative regulation of cell proliferation involved in contact inhibition / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / microtubule anchoring at centrosome / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / protein localization to cytoplasmic stress granule / Neutrophil degranulation / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / RHO GTPases Activate ROCKs / gamma-tubulin binding / dynein complex / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / regulation of axonogenesis / phosphorylation / RHOV GTPase cycle / oogenesis / 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 / establishment of mitotic spindle orientation / regulation of MAPK cascade / RHOU GTPase cycle / actin filament bundle assembly / 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 / centriole / 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 / transcription corepressor activity / disordered domain specific binding / cell-cell junction / cell migration / lamellipodium / positive regulation of protein phosphorylation / chromosome / actin cytoskeleton organization / protein autophosphorylation / spermatogenesis / nuclear membrane / microtubule / 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
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / p21 activated kinase binding domain / : ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase PAK 1 / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLightcap, C.M. / Williams, J.C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Biochemical and structural characterization of the Pak1-LC8 interaction.
Authors: Lightcap, C.M. / Sun, S. / Lear, J.D. / Rodeck, U. / Polenova, T. / Williams, J.C.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
C: P21 activated Kinase peptide
D: P21 activated Kinase peptide


Theoretical massNumber of molelcules
Total (without water)23,2964
Polymers23,2964
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-20 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.404, 57.378, 64.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / Cut up protein


Mass: 10603.067 Da / Num. of mol.: 2 / Mutation: K36P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): Plasmid / References: UniProt: Q24117
#2: Protein/peptide P21 activated Kinase peptide


Mass: 1045.124 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence represents a segment from naturally occurring protein in humans
References: UniProt: Q13153
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.89 Å3/Da / Density % sol: 34.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 200 mM NaCl, 27% (w/v) PEG 4000, and 10% 0.1 M (NH4)6CoCl3, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K, temperature 293K

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Data collection

Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: Onyx / Detector: DIFFRACTOMETER / Date: Nov 1, 2007
RadiationMonochromator: xenocs / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→11.65 Å / Num. obs: 6394 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.4.0034refinement
CrysalisProdata collection
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→11.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.061 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26283 299 4.7 %RANDOM
Rwork0.20403 ---
obs0.20687 6095 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→11.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 0 49 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.9372098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5015184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70324.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.57515260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.476156
X-RAY DIFFRACTIONr_chiral_restr0.0080.02226
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021188
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8321.5939
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44121514
X-RAY DIFFRACTIONr_scbond_it2.5293612
X-RAY DIFFRACTIONr_scangle_it3.944.5584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.467 30 -
Rwork0.208 407 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20090.3983-0.53114.7308-0.17711.90030.0331-0.08070.08420.087-0.00560.2623-0.064-0.2733-0.0275-0.17420.03060.0129-0.0042-0.0285-0.06735.7034.2320.648
22.2134-0.28520.92323.26160.20432.41850.00280.0077-0.08120.02670.0011-0.1535-0.03190.2272-0.0039-0.1809-0.00470.0171-0.01830.0262-0.053324.36-4.1790.443
36.7897-0.05980.02837.2044-3.901710.59540.03970.25420.1826-0.3135-0.3001-0.1238-1.16160.17210.2604-0.0834-0.01310.004-0.1304-0.04090.011717.35210.079-2.168
42.33871.0005-1.17883.94367.214520.2870.10560.1184-0.10070.0198-0.09360.00050.85460.2668-0.0119-0.04870.0114-0.0389-0.05740.02140.009912.622-10.006-2.513
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 897 - 91
2X-RAY DIFFRACTION2BB5 - 897 - 91
3X-RAY DIFFRACTION3CC213 - 2212 - 10
4X-RAY DIFFRACTION4DD213 - 2212 - 10

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