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- PDB-7qb0: Solution structure of paxillin LIM2/3 -

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Basic information

Entry
Database: PDB / ID: 7qb0
TitleSolution structure of paxillin LIM2/3
ComponentsIsoform Alpha of Paxillin
KeywordsCELL ADHESION / LIM domain / Zinc finger / integrin-binding
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 / 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.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPrestel, A. / Michaelis, M. / Klishin, N. / Moeller, H.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)RTG 2473 Germany
CitationJournal: To Be Published
Title: A flexible loop in the paxillin LIM3 domain mediates direct binding to integrin beta3
Authors: Baade, T. / Michaelis, M. / Prestel, A. / Paone, C. / Klishin, N. / Scheinost, L. / Nedielkov, R. / Hauck, C.R. / Moeller, H.M.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Isoform Alpha of Paxillin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0115
Polymers14,7501
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, The pattern of NOE-derived distance restraints confirms the formation of the coordination sphere of each of the four zinc ions., NMR Distance Restraints, Analysis ...Evidence: NMR Distance Restraints, The pattern of NOE-derived distance restraints confirms the formation of the coordination sphere of each of the four zinc ions., NMR Distance Restraints, Analysis of NMR chemical shifts indicates that N(delta1) of His 24, 27, 83, and 113, respectively, coordinate to the zinc ions.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform Alpha of Paxillin


Mass: 14749.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PXN / Plasmid: pET-24a / 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.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HNCA
171isotropic13D HBHA(CO)NH
181isotropic13D (H)CC(CO)NH
191isotropic13D H(CCCO)NH
1101isotropic13D NOESY-15N-HSQC
1111isotropic13D-NOESY-13Cali-HSQC
1121isotropic13D 1H-15N-NOE-HSQC
1132isotropic12D 1H-13C HSQC aliphatic
1142isotropic12D 1H-13C HSQC aromatic
1152isotropic13D (H)CCH-TOCSY
1162isotropic13D (H)CCH-TOCSY
1172isotropic13D (H)CCH-COSY
1182isotropic13D NOESY-13Cali-HSQC
1192isotropic13D NOESY-13Caro-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1500 uM [U-13C; U-15N] Paxillin LIM2/3, 150 mM sodium chloride, 50 mM sodium phosphate, 4 mM sodium azide, 1 mM DTT, 0.1 mM DSS, 95% H2O/5% D2OPaxillin LIM2/395% H2O/5% D2O
solution2500 uM [U-13C; U-15N] Paxillin LIM2/3, 150 mM sodium chloride, 50 mM sodium phosphate, 4 mM sodium azide, 1 mM DTT, 0.1 mM DSS, 100% D2OPaxillin LIM2/3100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMPaxillin LIM2/3[U-13C; U-15N]1
150 mMsodium chloridenatural abundance1
50 mMsodium phosphatenatural abundance1
4 mMsodium azidenatural abundance1
1 mMDTTnatural abundance1
0.1 mMDSSnatural abundance1
500 uMPaxillin LIM2/3[U-13C; U-15N]2
150 mMsodium chloridenatural abundance2
50 mMsodium phosphatenatural abundance2
4 mMsodium azidenatural abundance2
1 mMDTTnatural abundance2
0.1 mMDSSnatural abundance2
Sample conditionsIonic strength: 150mM NaCl mM / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: H/C/N-TCI cryo probe

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8.4.2Keller and Wuthrichchemical shift assignment
ATNOSHerrmann, Guntert and Wuthrichpeak picking
TALOS-NShen and Baxdata analysis
PyMOLDeLano Scientificdata analysis
TopSpin2.1-3.1Bruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing8
simulated annealing7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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