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- PDB-2kbx: Solution structure of ILK-PINCH complex -

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Basic information

Entry
Database: PDB / ID: 2kbx
TitleSolution structure of ILK-PINCH complex
Components
  • Integrin-linked protein kinase
  • LIM and senescent cell antigen-like-containing domain protein 1
KeywordsCELL ADHESION / cytoskeletal regulators / ANK repeat / ATP-binding / Cell junction / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Acetylation / LIM domain / Metal-binding / Zinc
Function / homology
Function and homology information


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 / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / fibroblast migration / Cell-extracellular matrix interactions ...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 / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / fibroblast migration / Cell-extracellular matrix interactions / myelination in peripheral nervous system / cell projection organization / establishment or maintenance of epithelial cell apical/basal polarity / cell-cell junction organization / positive regulation of BMP signaling pathway / positive regulation of cell-substrate adhesion / neural precursor cell proliferation / branching involved in ureteric bud morphogenesis / outflow tract morphogenesis / positive regulation of focal adhesion assembly / positive regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / positive regulation of GTPase activity / mitotic spindle organization / sarcomere / cell-matrix adhesion / integrin-mediated signaling pathway / establishment of protein localization / cell morphogenesis / cell-cell adhesion / platelet aggregation / positive regulation of canonical Wnt signaling pathway / integrin binding / cell-cell junction / lamellipodium / actin binding / cell cortex / protein-macromolecule adaptor activity / positive regulation of canonical NF-kappaB signal transduction / cell differentiation / protein kinase activity / signaling receptor binding / focal adhesion / negative regulation of DNA-templated transcription / centrosome / positive regulation of cell population proliferation / positive regulation of gene expression / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / magnesium ion binding / zinc ion binding / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin-linked protein kinase, pseudokinase domain / LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...Integrin-linked protein kinase, pseudokinase domain / LIM and senescent cell antigen-like-containing domain protein 1-like / : / : / Cysteine Rich Protein / Cysteine Rich Protein / 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. / : / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ribbon / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
LIM and senescent cell antigen-like-containing domain protein 1 / Scaffold protein ILK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 2
AuthorsQin, J.
CitationJournal: To be Published
Title: Cytosketal proteins
Authors: Qin, J.
History
DepositionDec 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin-linked protein kinase
B: LIM and senescent cell antigen-like-containing domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4744
Polymers27,3432
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 19379.928 Da / Num. of mol.: 1 / Fragment: N-terminal domain
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 LIM and senescent cell antigen-like-containing domain protein 1 / Particularly interesting new Cys-His protein 1 / PINCH-1 / Renal carcinoma antigen NY-REN-48


Mass: 7963.024 Da / Num. of mol.: 1 / Fragment: LIM zinc-binding 1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1, PINCH, PINCH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P48059
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.1-0.5 mM [U-100% 15N] Integrin-linked protein kinase, 0.1-0.5 mM [U-100% 13C; U-100% 15N] LIM and senescent cell antigen-like-containing domain protein 1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-100% 15N]0.1-0.51
mMentity_1-2[U-100% 13C; U-100% 15N]0.1-0.51
Sample conditionsIonic strength: 50mM / pH: 6.5 / Pressure: ambient / Temperature: 30 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: C-N bond distance between PHE 42 and GLN 43 chain B is in the range of 1.16-1.21A in all models.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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