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- PDB-6mif: Lim5 domain of PINCH1 protein -

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Basic information

Entry
Database: PDB / ID: 6mif
TitleLim5 domain of PINCH1 protein
ComponentsLIM and senescent cell antigen-like-containing domain protein 1
KeywordsSIGNALING PROTEIN / Lim domain / Zn binding
Function / homology
Function and homology information


Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of integrin-mediated signaling pathway / Cell-extracellular matrix interactions / cell-cell junction organization / positive regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / establishment of protein localization ...Regulation of cytoskeletal remodeling and cell spreading by IPP complex components / positive regulation of integrin-mediated signaling pathway / Cell-extracellular matrix interactions / cell-cell junction organization / positive regulation of cell-substrate adhesion / positive regulation of focal adhesion assembly / positive regulation of substrate adhesion-dependent cell spreading / cellular response to transforming growth factor beta stimulus / tumor necrosis factor-mediated signaling pathway / establishment of protein localization / cell-cell adhesion / positive regulation of GTPase activity / cell-cell junction / positive regulation of canonical NF-kappaB signal transduction / focal adhesion / negative regulation of DNA-templated transcription / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / : / 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
LIM and senescent cell antigen-like-containing domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsQin, J. / Vaynberg, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL058758 United States
CitationJournal: Nat Commun / Year: 2018
Title: Non-catalytic signaling by pseudokinase ILK for regulating cell adhesion.
Authors: Vaynberg, J. / Fukuda, K. / Lu, F. / Bialkowska, K. / Chen, Y. / Plow, E.F. / Qin, J.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
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 / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM and senescent cell antigen-like-containing domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1263
Polymers8,9951
Non-polymers1312
Water0
1


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

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Components

#1: Protein LIM and senescent cell antigen-like-containing domain protein 1 / Particularly interesting new Cys-His protein 1 / PINCH-1 / Renal carcinoma antigen NY-REN-48


Mass: 8994.751 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMS1, PINCH, PINCH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P48059
#2: Chemical ChemComp-ZN / ZINC ION


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

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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
182isotropic12D 1H-15N HSQC
122isotropic13D HNCO
132isotropic13D HNCA
142isotropic13D CBCA(CO)NH
152isotropic13D (H)CCH-TOCSY
162isotropic13D HN(CA)CB
172isotropic13D HNHA
192isotropic13D C(CO)NH
1102isotropic13D 1H-15N NOESY
1112isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] Lim5-T, 90% H2O/10% D2O15N Lim5-T90% H2O/10% D2O
solution21.0 mM [U-13C; U-15N] 15N 13C Lim5-T, 90% H2O/10% D2O15N 13C Lim5-T90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMLim5-T[U-15N]1
1.0 mM15N 13C Lim5-T[U-13C; U-15N]2
Sample conditionsDetails: 20mM NaH2PO4, 20mM NaCl, 0.1mM TCEP / Ionic strength: 20mM NaCl mM / Label: NMR buffer / pH: 6.5 / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
PIPPGarrettpeak picking
XwinNMRBruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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