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- PDB-2k2r: The NMR structure of alpha-parvin CH2/paxillin LD1 complex -

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Basic information

Entry
Database: PDB / ID: 2k2r
TitleThe NMR structure of alpha-parvin CH2/paxillin LD1 complex
Components
  • Alpha-parvin
  • Paxillin
KeywordsCELL ADHESION / Protein complex / Actin-binding / Alternative splicing / Cell junction / Cytoplasm / Cytoskeleton / LIM domain / Metal-binding / Phosphoprotein / Zinc
Function / homology
Function and homology information


actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion ...actin-mediated cell contraction / smooth muscle cell chemotaxis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / Cell-extracellular matrix interactions / neuropilin binding / outflow tract septum morphogenesis / signal complex assembly / heterotypic cell-cell adhesion / sprouting angiogenesis / microtubule associated complex / growth hormone receptor signaling pathway / establishment or maintenance of cell polarity / protein kinase inhibitor activity / cilium assembly / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / stress fiber / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / Z disc / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / actin cytoskeleton / lamellipodium / actin binding / cell cortex / regulation of cell shape / actin cytoskeleton organization / protein phosphatase binding / protein stabilization / cell adhesion / cadherin binding / focal adhesion / signal transduction / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Parvin / Paxillin / : / : / Paxillin family / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...Parvin / Paxillin / : / : / Paxillin family / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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. / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Paxillin / Alpha-parvin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Fukuda, K. / Byeon, I. / Velyvis, A. / Wu, C. / Gronenborn, A. / Qin, J.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Structure of {alpha}-Parvin CH2-Paxillin LD1 Complex Reveals a Novel Modular Recognition for Focal Adhesion Assembly.
Authors: Wang, X. / Fukuda, K. / Byeon, I.J. / Velyvis, A. / Wu, C. / Gronenborn, A. / Qin, J.
History
DepositionApr 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 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_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-parvin
B: Paxillin


Theoretical massNumber of molelcules
Total (without water)16,0982
Polymers16,0982
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Alpha-parvin / Calponin-like integrin-linked kinase-binding protein / CH-ILKBP / Actopaxin


Mass: 15011.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species: sapiens / Gene: PARVA / Plasmid: pET3a / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVD7
#2: Protein/peptide Paxillin /


Mass: 1087.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P49023*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D C(CO)NH
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1613D 1H-13C NOESY
1713D 1H-15N NOESY
1812D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.25 mM [U-13C; U-15N] entity_1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.25 mM / Component: entity_1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 130 / pH: 7.2 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker N/A / Manufacturer: Bruker / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHBrungerstructure solution
X-PLOR NIHBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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