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- PDB-3kmw: Crystal structure of the ILK/alpha-parvin core complex (MgATP) -

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Basic information

Entry
Database: PDB / ID: 3kmw
TitleCrystal structure of the ILK/alpha-parvin core complex (MgATP)
Components
  • Alpha-parvin
  • Integrin-linked kinase
KeywordsCELL ADHESION / ANK repeat / ATP-binding / Cell junction / Cell membrane / Integrin-binding protein / Membrane / Nucleotide-binding / Phosphoprotein / Pseudokinase / Actin-binding / Alternative splicing / Cytoplasm / Cytoskeleton
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / protein localization to cell cortex / caveola assembly / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / nerve development ...actin-mediated cell contraction / smooth muscle cell chemotaxis / establishment or maintenance of cell polarity regulating cell shape / protein localization to cell cortex / caveola assembly / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / 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 / myelination in peripheral nervous system / positive regulation of BMP signaling pathway / cell projection organization / outflow tract septum morphogenesis / sprouting angiogenesis / neural precursor cell proliferation / 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 / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / sarcomere / cell-matrix adhesion / tumor necrosis factor-mediated signaling pathway / mitotic spindle organization / integrin-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / platelet aggregation / integrin binding / Z disc / cell morphogenesis / positive regulation of canonical Wnt signaling pathway / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / cell cortex / protein-macromolecule adaptor activity / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / 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 / cytoplasm / cytosol
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
ADENOSINE-5'-TRIPHOSPHATE / Scaffold protein ILK / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFukuda, K. / Qin, J.
CitationJournal: Mol.Cell / Year: 2009
Title: The pseudoactive site of ILK is essential for its binding to alpha-Parvin and localization to focal adhesions.
Authors: Fukuda, K. / Gupta, S. / Chen, K. / Wu, C. / Qin, J.
History
DepositionNov 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin-linked kinase
B: Alpha-parvin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3474
Polymers45,8152
Non-polymers5312
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.134, 117.103, 47.393
Angle α, β, γ (deg.)90.00, 101.96, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe heterodimeric complex observed in the asymmetric unit is relevant to the biological assembly unit in vivo.

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Components

#1: Protein Integrin-linked kinase / ILK


Mass: 30972.014 Da / Num. of mol.: 1
Fragment: C-terminal pseudokinase domain: UNP residues 183-452
Mutation: C346S, C422S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILK, ILK1, ILK2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13418
#2: Protein Alpha-parvin / Calponin-like integrin-linked kinase-binding protein / CH-ILKBP / Matrix-remodeling-associated ...Calponin-like integrin-linked kinase-binding protein / CH-ILKBP / Matrix-remodeling-associated protein 2 / Actopaxin


Mass: 14843.072 Da / Num. of mol.: 1
Fragment: C-terminal calponin homology domain: UNP residues 248-372
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARVA, MXRA2 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9NVD7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.62 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 277 K / pH: 6.8
Details: 0.05 M Bis-Tris, 12% PEG 5000 MME, 5% 1-propyl alcohol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→46.36 Å / Num. obs: 31165 / % possible obs: 98.3 % / Redundancy: 5.53 % / Rsym value: 0.098 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.09 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.136 / % possible all: 98.8

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Processing

Software
NameClassification
StructureStudiodata collection
AMoREphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KMU

3kmu


Resolution: 2→46.36 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1539 -RANDOM
Rwork0.199 ---
obs0.199 31052 98 %-
Refinement stepCycle: LAST / Resolution: 2→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 32 309 3498
LS refinement shellResolution: 2→2.02 Å /
RfactorNum. reflection
Rfree0.2475 51
Rwork0.2296 -

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