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- PDB-6u4n: Solution structure of paxillin LIM4 in complex with kindlin-2 F0 -

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Basic information

Entry
Database: PDB / ID: 6u4n
TitleSolution structure of paxillin LIM4 in complex with kindlin-2 F0
Components
  • Fermitin family homolog 2
  • Paxillin
KeywordsCELL ADHESION / LIM domain / Zinc finger / Ubiquitin fold / Complex
Function / homology
Function and homology information


adherens junction maintenance / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / 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 / vinculin binding / positive regulation of integrin activation / Cell-extracellular matrix interactions ...adherens junction maintenance / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / 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 / vinculin binding / positive regulation of integrin activation / Cell-extracellular matrix interactions / type I transforming growth factor beta receptor binding / neuropilin binding / integrin activation / focal adhesion assembly / signal complex assembly / protein localization to membrane / negative regulation of vascular permeability / regulation of cell morphogenesis / I band / limb development / microtubule associated complex / growth hormone receptor signaling pathway / negative regulation of fat cell differentiation / SMAD binding / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of focal adhesion assembly / lamellipodium membrane / endothelial cell migration / Smooth Muscle Contraction / positive regulation of epithelial to mesenchymal transition / RAC3 GTPase cycle / positive regulation of osteoblast differentiation / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / stress fiber / positive regulation of stress fiber assembly / RAC1 GTPase cycle / extrinsic component of cytoplasmic side of plasma membrane / substrate adhesion-dependent cell spreading / cell-matrix adhesion / transforming growth factor beta receptor signaling pathway / integrin-mediated signaling pathway / adherens junction / cytoplasmic side of plasma membrane / beta-catenin binding / Wnt signaling pathway / cellular response to reactive oxygen species / positive regulation of GTPase activity / VEGFA-VEGFR2 Pathway / positive regulation of protein localization to nucleus / actin filament binding / cell-cell junction / cell migration / integrin binding / lamellipodium / cell junction / actin binding / cell cortex / regulation of cell shape / protein phosphatase binding / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / focal adhesion / protein kinase binding / cell surface / signal transduction / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Paxillin / : / : / Paxillin family / Cysteine Rich Protein / Cysteine Rich Protein ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / Paxillin / : / : / Paxillin family / 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. / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ubiquitin-like (UB roll) / Ribbon / PH-like domain superfamily / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Paxillin / Fermitin family homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsZhu, L. / Qin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Structure / Year: 2019
Title: Structural Basis of Paxillin Recruitment by Kindlin-2 in Regulating Cell Adhesion.
Authors: Zhu, L. / Liu, H. / Lu, F. / Yang, J. / Byzova, T.V. / Qin, J.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 2
B: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4434
Polymers21,3122
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1060 Å2
ΔGint-9 kcal/mol
Surface area10660 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein 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: 13002.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT2, KIND2, MIG2, PLEKHC1 / Plasmid: pGST-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96AC1
#2: Protein Paxillin /


Mass: 8309.760 Da / Num. of mol.: 1 / Fragment: LIM4 domain residues 527-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: pGST-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P49023
#3: Chemical ChemComp-ZN / ZINC ION


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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 15N/13C-edited NOESY
122isotropic13D 15N/13C-edited NOESY
233isotropic13D 15N/13C-filtered NOESY
244isotropic13D 15N/13C-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 95% H2O/5% D2O0.55 mM 15N/13C-labeled paxillin LIM4 in the presence of 0.89 mM unlabeled kindlin-2 F015N, 13C_195% H2O/5% D2O
solution20.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 95% H2O/5% D2O0.54 mM 15N/13C- labeled kindlin-2 F0 in the presence of 0.85 mM unlabeled paxillin LIM415N, 13C_295% H2O/5% D2O
solution30.55 mM U-15N, U-13C paxillin LIM4, 0.89 mM kindlin-2 F0, 99.8% D2O0.55 mM 15N/13C-labeled paxillin LIM4 in the presence of 0.89 mM unlabeled kindlin-2 F0 prepared in 99.8% D2O15N, 13C_399.8% D2O
solution40.54 mM U-15N, U-13C kindlin-2 F0, 0.85 mM paxillin LIM4, 99.8% D2O0.54 mM 15N/13C- labeled kindlin-2 F0 in the presence of 0.85 mM unlabeled paxillin LIM4 prepared in 99.8% D2O15N, 13C_499.8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.55 mMpaxillin LIM4U-15N, U-13C1
0.89 mMkindlin-2 F0natural abundance1
0.54 mMkindlin-2 F0U-15N, U-13C2
0.85 mMpaxillin LIM4natural abundance2
0.55 mMpaxillin LIM4U-15N, U-13C3
0.89 mMkindlin-2 F0natural abundance3
0.54 mMkindlin-2 F0U-15N, U-13C4
0.85 mMpaxillin LIM4natural abundance4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM NaH2PO4/Na2HPO4 (pH 6.8), 50 mM NaCl, 0.5 mM TCEP and 5% D2O50 mM NaCl mMconditions_16.8 ambient Pa298 K
250 mM NaH2PO4/Na2HPO4 (pH 6.8), 50 mM NaCl, 0.5 mM TCEP in 99.8% D2O50 mM NaCl mMconditions_26.8 ambient Pa298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
PIPPGarrettpeak picking
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
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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