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- PDB-2msu: NMR structure of Kindlin-2 F2 339-358 -

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Basic information

Entry
Database: PDB / ID: 2msu
TitleNMR structure of Kindlin-2 F2 339-358
ComponentsFermitin family homolog 2
KeywordsCELL ADHESION / focal adhesion / ILK / integrin
Function / homology
Function and homology information


adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / protein localization to membrane ...adherens junction maintenance / positive regulation of myosin light chain kinase activity / protein localization to cell junction / positive regulation of mesenchymal stem cell proliferation / positive regulation of wound healing, spreading of epidermal cells / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / integrin activation / protein localization to membrane / focal adhesion assembly / negative regulation of vascular permeability / regulation of cell morphogenesis / I band / limb development / negative regulation of fat cell differentiation / SMAD binding / positive regulation of focal adhesion assembly / phosphatidylinositol-3,4,5-trisphosphate binding / lamellipodium membrane / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / stress fiber / positive regulation of substrate adhesion-dependent cell spreading / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of stress fiber assembly / RAC1 GTPase cycle / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / positive regulation of GTPase activity / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / Wnt signaling pathway / positive regulation of protein localization to nucleus / actin filament binding / integrin binding / cell junction / actin binding / cell cortex / regulation of cell shape / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell adhesion / positive regulation of cell migration / focal adhesion / protein kinase binding / cell surface / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Fermitin family homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsFukuda, K. / Bledzka, K. / Yang, J. / Perera, H.D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular Basis of Kindlin-2 Binding to Integrin-linked Kinase Pseudokinase for Regulating Cell Adhesion.
Authors: Fukuda, K. / Bledzka, K. / Yang, J. / Perera, H.D. / Plow, E.F. / Qin, J.
History
DepositionAug 5, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 2


Theoretical massNumber of molelcules
Total (without water)2,1921
Polymers2,1921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 99structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Fermitin family homolog 2 / Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family ...Kindlin-2 / Mitogen-inducible gene 2 protein / MIG-2 / Pleckstrin homology domain-containing family C member 1 / PH domain-containing family C member 1


Mass: 2192.309 Da / Num. of mol.: 1 / Fragment: UNP residues 339-358
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT2, KIND2, MIG2, PLEKHC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96AC1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 20 mM HEPES, 100 mM sodium chloride, 2 mM DTT, 2 mM K2F2 peptide, 50 uM ILK KLD/a-parvin CH2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMHEPES-11
100 mMsodium chloride-21
2 mMDTT-31
2 mMK2F2 peptide-41
50 uMILK KLD/a-parvin CH2-51
Sample conditionsIonic strength: 100 / pH: 6.8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorestructure solution
XPLOR-NIH2.25Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 267 / NOE intraresidue total count: 79 / NOE long range total count: 0 / NOE medium range total count: 61 / NOE sequential total count: 127
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 99 / Conformers submitted total number: 19

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