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- PDB-5l6w: Structure Of the LIMK1-ATPgammaS-CFL1 Complex -

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Basic information

Entry
Database: PDB / ID: 5l6w
TitleStructure Of the LIMK1-ATPgammaS-CFL1 Complex
Components
  • Cofilin-1
  • LIM domain kinase 1
KeywordsTRANSFERASE / kinase complex
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of embryonic development / positive regulation of actin filament bundle assembly / actin filament severing / establishment of spindle localization / regulation of dendritic spine morphogenesis / actin filament depolymerization / positive regulation by host of viral process / RHO GTPases Activate ROCKs / regulation of cell morphogenesis ...actin filament fragmentation / positive regulation of embryonic development / positive regulation of actin filament bundle assembly / actin filament severing / establishment of spindle localization / regulation of dendritic spine morphogenesis / actin filament depolymerization / positive regulation by host of viral process / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / Sema4D induced cell migration and growth-cone collapse / axon extension / stress fiber assembly / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / mitotic cytokinesis / lamellipodium membrane / ubiquitin ligase inhibitor activity / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / positive regulation of axon extension / positive regulation of stress fiber assembly / heat shock protein binding / cytoskeleton organization / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / male germ cell nucleus / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / actin filament binding / Platelet degranulation / nervous system development / lamellipodium / actin cytoskeleton / actin cytoskeleton organization / growth cone / vesicle / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 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 / postsynapse / protein kinase activity / neuron projection / nuclear speck / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / glutamatergic synapse / signal transduction / extracellular space / extracellular exosome / ATP binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / LIM zinc-binding domain signature. / Severin / Severin / LIM domain ...: / ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / LIM zinc-binding domain signature. / Severin / Severin / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / ADF-H/Gelsolin-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Cofilin-1 / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSalah, E. / Mathea, S. / Oerum, S. / Newman, J.A. / Tallant, C. / Adamson, R. / Canning, P. / Beltrami, A. / von Delft, F. / Arrowsmith, C.H. ...Salah, E. / Mathea, S. / Oerum, S. / Newman, J.A. / Tallant, C. / Adamson, R. / Canning, P. / Beltrami, A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Bullock, A.N.
CitationJournal: To Be Published
Title: Structure Of the LIMK1-ATPgammaS-CFL1 Complex
Authors: Salah, E. / Bullock, A.N.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: LIM domain kinase 1
C: Cofilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1543
Polymers54,6302
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-16 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.679, 80.679, 237.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LIM domain kinase 1 / LIMK-1


Mass: 35994.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18635.674 Da / Num. of mol.: 1 / Mutation: S3C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli (E. coli) / References: UniProt: P23528
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 35% pentaerythritol propoxylate 5/4, 0.1 M HEPES pH 7.5, 0.2 M potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.53→34.94 Å / Num. obs: 30888 / % possible obs: 100 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q8G, 3S95

1q8g

3s95


Resolution: 2.53→34.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.737 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28395 1489 4.8 %RANDOM
Rwork0.22614 ---
obs0.22889 29335 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.725 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å21.59 Å2-0 Å2
2--3.19 Å2-0 Å2
3----10.34 Å2
Refinement stepCycle: 1 / Resolution: 2.53→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 31 0 3398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193476
X-RAY DIFFRACTIONr_bond_other_d0.0020.023132
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.964735
X-RAY DIFFRACTIONr_angle_other_deg1.07637170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9335452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25424.031129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1615522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5691513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214005
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02764
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_it7.5769.4241818
X-RAY DIFFRACTIONr_mcbond_other7.5679.4211816
X-RAY DIFFRACTIONr_mcangle_it10.57114.1212266
X-RAY DIFFRACTIONr_mcangle_other10.56914.1242267
X-RAY DIFFRACTIONr_scbond_it8.3939.5081658
X-RAY DIFFRACTIONr_scbond_other8.3849.5091658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.16814.1482470
X-RAY DIFFRACTIONr_long_range_B_refined13.43574.8943938
X-RAY DIFFRACTIONr_long_range_B_other13.44474.8873938
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 81 -
Rwork0.426 2139 -
obs--99.95 %

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