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- PDB-6u4m: Solution structure of paxillin LIM4 -

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Basic information

Entry
Database: PDB / ID: 6u4m
TitleSolution structure of paxillin LIM4
ComponentsPaxillin
KeywordsCELL ADHESION / LIM domain / Zinc finger
Function / homology
Function and homology information


Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / endothelial cell migration / Smooth Muscle Contraction / GAB1 signalosome ...Localization of the PINCH-ILK-PARVIN complex to focal adhesions / Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / vinculin binding / neuropilin binding / signal complex assembly / microtubule associated complex / growth hormone receptor signaling pathway / 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 / beta-catenin binding / cellular response to reactive oxygen species / VEGFA-VEGFR2 Pathway / cell-cell junction / cell migration / lamellipodium / cell cortex / protein phosphatase binding / cell adhesion / focal adhesion / signal transduction / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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 ...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. / Ribbon / Mainly Beta
Similarity search - Domain/homology
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
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4413
Polymers8,3101
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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
#2: 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 HNCO
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D CC(CO)NH
151isotropic13D (H)CCH-TOCSY
171isotropic23D (H)CC(CO)NH
161isotropic13D 15N/13C-edited NOESY

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Sample preparation

DetailsType: solution
Contents: 1.45 mM [U-13C; U-15N] Paxillin LIM4, 95% H2O/5% D2O
Label: 15N, 13C / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.45 mM / Component: Paxillin LIM4 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 50 mM NaH2PO4/Na2HPO4 (pH 6.8), 50 mM NaCl, 0.5 mM TCEP and 5% D2O
Ionic strength: 50mM NaCl mM / Label: conditions_1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
PIPPGarrettpeak picking
PASAXu, Wang, Yang, Vaynberg, and Qinchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
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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