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- PDB-6mib: Crystal structure of the ILK ATP-binding deficient mutant (L207W)... -

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Basic information

Entry
Database: PDB / ID: 6mib
TitleCrystal structure of the ILK ATP-binding deficient mutant (L207W)/alpha-parvin core complex
Components
  • Alpha-parvin
  • Integrin-linked protein kinase
KeywordsCELL ADHESION / Pseudokinase / Protein complex
Function / homology
Function and homology information


smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / caveola assembly / protein localization to cell cortex / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / actin-mediated cell contraction / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development ...smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / caveola assembly / protein localization to cell cortex / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / actin-mediated cell contraction / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development / fibroblast migration / establishment or maintenance of epithelial cell apical/basal polarity / Cell-extracellular matrix interactions / cell projection organization / myelination in peripheral nervous system / outflow tract septum morphogenesis / positive regulation of BMP signaling pathway / neural precursor cell proliferation / sprouting angiogenesis / heterotypic cell-cell adhesion / branching involved in ureteric bud morphogenesis / establishment or maintenance of cell polarity / protein kinase inhibitor activity / outflow tract morphogenesis / cilium assembly / positive regulation of osteoblast differentiation / tumor necrosis factor-mediated signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / sarcomere / cell-matrix adhesion / mitotic spindle organization / integrin-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell morphogenesis / Z disc / platelet aggregation / integrin binding / positive regulation of canonical Wnt signaling pathway / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / protein kinase activity / protein stabilization / cadherin binding / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / centrosome / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / magnesium ion binding / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin-linked protein kinase, pseudokinase domain / Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain / : / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...Integrin-linked protein kinase, pseudokinase domain / Parvin / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / Calponin homology (CH) domain / : / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Scaffold protein ILK / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFukuda, K. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Nat Commun / Year: 2018
Title: Non-catalytic signaling by pseudokinase ILK for regulating cell adhesion.
Authors: Vaynberg, J. / Fukuda, K. / Lu, F. / Bialkowska, K. / Chen, Y. / Plow, E.F. / Qin, J.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin-linked protein kinase
B: Alpha-parvin


Theoretical massNumber of molelcules
Total (without water)45,8882
Polymers45,8882
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Co-expression
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-11 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.714, 117.635, 47.775
Angle α, β, γ (deg.)90.00, 114.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Integrin-linked protein kinase / 59 kDa serine/threonine-protein kinase / ILK-1 / ILK-2 / p59ILK


Mass: 31045.064 Da / Num. of mol.: 1 / Mutation: L207W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13418, non-specific serine/threonine protein kinase
#2: Protein Alpha-parvin / Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling- ...Actopaxin / CH-ILKBP / Calponin-like integrin-linked kinase-binding protein / Matrix-remodeling-associated protein 2


Mass: 14843.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVD7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% PEG 3,350, 0.1 M Bis-Tris Propane, pH 7.4, 5% 1-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39797 / % possible obs: 98.9 % / Redundancy: 4.6 % / Net I/σ(I): 41.78
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 7.69 / Num. unique obs: 1954 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.186 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.115 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20778 2066 5.2 %RANDOM
Rwork0.16016 ---
obs0.16259 37699 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.898 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.08 Å2
2--0.35 Å20 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.8→20.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 0 223 3403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193264
X-RAY DIFFRACTIONr_bond_other_d0.0020.023156
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9624424
X-RAY DIFFRACTIONr_angle_other_deg1.06337280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13324.054148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12415576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1011519
X-RAY DIFFRACTIONr_chiral_restr0.1320.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213612
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
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_it2.3511.9811574
X-RAY DIFFRACTIONr_mcbond_other2.3471.9781573
X-RAY DIFFRACTIONr_mcangle_it3.5162.951964
X-RAY DIFFRACTIONr_mcangle_other3.5172.9521965
X-RAY DIFFRACTIONr_scbond_it3.5062.4321690
X-RAY DIFFRACTIONr_scbond_other3.4972.4241687
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4453.482459
X-RAY DIFFRACTIONr_long_range_B_refined6.92916.3593737
X-RAY DIFFRACTIONr_long_range_B_other6.90116.1653653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 145 -
Rwork0.191 2612 -
obs--92.27 %

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