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- PDB-5hvj: Crystal structure of LIMK1 D460N mutant in complex with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 5hvj
TitleCrystal structure of LIMK1 D460N mutant in complex with AMP-PNP
ComponentsLIM domain kinase 1
KeywordsTRANSFERASE / kinase ATP analog actin-remodeling
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / nuclear speck / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHamill, S. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases.
Authors: Hamill, S. / Lou, H.J. / Turk, B.E. / Boggon, T.J.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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
A: LIM domain kinase 1
B: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2933
Polymers72,7862
Non-polymers5061
Water1,26170
1
A: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8992
Polymers36,3931
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIM domain kinase 1


Theoretical massNumber of molelcules
Total (without water)36,3931
Polymers36,3931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.987, 59.573, 98.276
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36393.211 Da / Num. of mol.: 2 / Mutation: D460N
Source method: isolated from a genetically manipulated source
Details: Optimized cDNA / Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 18-24% PEG 3350, 0.2 M potassium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→39.979 Å / Num. obs: 31929 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.156 / Net I/av σ(I): 12.8 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S95

3s95


Resolution: 2.2→39.979 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1613 5.07 %Random
Rwork0.2057 ---
obs0.208 31815 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 75.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4609 0 19 70 4698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024772
X-RAY DIFFRACTIONf_angle_d0.6416450
X-RAY DIFFRACTIONf_dihedral_angle_d12.9051818
X-RAY DIFFRACTIONf_chiral_restr0.027688
X-RAY DIFFRACTIONf_plane_restr0.003831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.44011450.37712397X-RAY DIFFRACTION98
2.2648-2.33790.35861240.32192535X-RAY DIFFRACTION100
2.3379-2.42140.36061450.29312481X-RAY DIFFRACTION100
2.4214-2.51840.37181360.28622501X-RAY DIFFRACTION100
2.5184-2.6330.30311510.25382500X-RAY DIFFRACTION100
2.633-2.77170.34571130.24512526X-RAY DIFFRACTION100
2.7717-2.94530.29171310.24172512X-RAY DIFFRACTION100
2.9453-3.17270.25631380.22272521X-RAY DIFFRACTION100
3.1727-3.49180.25541260.20342544X-RAY DIFFRACTION100
3.4918-3.99670.21241400.18232521X-RAY DIFFRACTION100
3.9967-5.03380.21691270.1592564X-RAY DIFFRACTION100
5.0338-39.98530.20151370.17692600X-RAY DIFFRACTION100
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)
18.75731.756-2.56597.3386-1.04179.2455-0.1753-0.6475-0.10370.66110.1373-0.3669-0.3130.32620.13070.590.0351-0.20190.51720.0170.755512.32493.5468-7.8488
28.6241.58453.96342.03320.60458.3048-0.1564-1.3225-0.30471.11070.3280.1251-0.2819-0.1818-0.1960.66570.0944-0.00350.8160.17960.79470.99482.43492.9264
35.5747-1.33842.11972.4284-0.96014.7809-0.00330.0359-0.17580.16640.0972-0.2730.06390.4317-0.03080.367-0.0132-0.04840.25960.00540.5372-4.47054.7171-13.3785
45.0622-3.88240.70576.35820.15366.5249-0.5113-0.78830.07771.15280.0944-0.31130.0513-0.31540.42820.7617-0.0314-0.11590.5399-0.03560.5293-13.579110.0971.3184
53.7026-0.26980.11887.2774-2.30798.0751-0.2569-0.19820.2340.0336-0.02940.3295-0.495-0.35410.24230.37880.0041-0.12360.2619-0.02480.6233-20.921616.7224-13.2525
63.2012-1.20640.81416.13243.49852.74850.105-0.3359-0.67280.2779-0.20790.58860.7751-0.18950.330.3769-0.0947-0.09750.29770.05140.6806-22.80372.8808-15.4097
74.5458-1.585-3.79398.69476.45859.2754-0.1506-0.103-0.1533-0.3207-0.13621.0227-0.3179-0.2280.27890.4707-0.037-0.16830.36160.00820.8258-32.1127.2161-21.942
85.3283-1.339-0.21274.10920.26537.58080.56261.3019-0.1608-0.9892-0.93050.13970.4553-0.08380.41491.04970.3718-0.30731.18240.0390.869-41.8656-10.6852-56.8454
94.6348-1.42411.16243.615-0.45663.22160.4550.4096-0.1034-0.6931-0.26550.46670.4549-0.2711-0.19650.7109-0.0466-0.22840.41440.00470.6356-31.7934-18.1928-39.9344
102.2349-1.92490.98665.8099-1.36962.39050.066-0.01250.19410.248-0.0743-0.6774-0.01350.08130.03090.563-0.0516-0.12340.3167-0.05260.6498-19.8752-17.9072-25.0788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 329 through 374 )
2X-RAY DIFFRACTION2chain 'A' and (resid 375 through 390 )
3X-RAY DIFFRACTION3chain 'A' and (resid 391 through 476 )
4X-RAY DIFFRACTION4chain 'A' and (resid 477 through 527 )
5X-RAY DIFFRACTION5chain 'A' and (resid 528 through 586 )
6X-RAY DIFFRACTION6chain 'A' and (resid 587 through 613 )
7X-RAY DIFFRACTION7chain 'A' and (resid 614 through 633 )
8X-RAY DIFFRACTION8chain 'B' and (resid 330 through 390 )
9X-RAY DIFFRACTION9chain 'B' and (resid 391 through 569 )
10X-RAY DIFFRACTION10chain 'B' and (resid 570 through 637 )

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