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- PDB-6ut2: 3D structure of the leiomodin/tropomyosin binding interface -

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Basic information

Entry
Database: PDB / ID: 6ut2
Title3D structure of the leiomodin/tropomyosin binding interface
Components
  • Leiomodin-2
  • Tropomyosin alpha-1 chain chimeric peptide
KeywordsSTRUCTURAL PROTEIN / pointed end / thin filaments
Function / homology
Function and homology information


pointed-end actin filament capping / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / myofibril assembly / actin nucleation / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / ruffle organization ...pointed-end actin filament capping / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / myofibril assembly / actin nucleation / bleb / negative regulation of vascular associated smooth muscle cell migration / regulation of muscle contraction / muscle filament sliding / ruffle organization / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of ATP-dependent activity / Striated Muscle Contraction / M band / structural constituent of muscle / ventricular cardiac muscle tissue morphogenesis / regulation of heart contraction / sarcomere organization / myofibril / positive regulation of actin filament polymerization / tropomyosin binding / striated muscle thin filament / positive regulation of cell adhesion / actin monomer binding / Smooth Muscle Contraction / muscle contraction / cardiac muscle contraction / stress fiber / positive regulation of stress fiber assembly / cytoskeleton organization / cytoskeletal protein binding / actin filament polymerization / sarcomere / negative regulation of cell migration / actin filament organization / actin filament / ruffle membrane / wound healing / cellular response to reactive oxygen species / structural constituent of cytoskeleton / actin filament binding / actin cytoskeleton / actin binding / regulation of cell shape / cytoskeleton / protein heterodimerization activity / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Tropomodulin / Tropomodulin / WH2 domain / WH2 domain profile. / Tropomyosins signature. / Tropomyosin / Tropomyosin / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Tropomyosin alpha-1 chain / Leiomodin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsTolkatchev, D. / Smith, G.E. / Helms, G.L. / Cort, J.R. / Kostyukova, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM120137-02 United States
CitationJournal: Plos Biol. / Year: 2020
Title: Leiomodin creates a leaky cap at the pointed end of actin-thin filaments.
Authors: Tolkatchev, D. / Smith Jr., G.E. / Schultz, L.E. / Colpan, M. / Helms, G.L. / Cort, J.R. / Gregorio, C.C. / Kostyukova, A.S.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leiomodin-2
B: Tropomyosin alpha-1 chain chimeric peptide
C: Tropomyosin alpha-1 chain chimeric peptide


Theoretical massNumber of molelcules
Total (without water)12,4883
Polymers12,4883
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, homologous to known tropomyosin-binding sites of tropomodulins, Circular dichroism and NMR experiments to characterize the assembly are in Colpan et al, Biochim Biophys Acta. 2016 May; 1864(5), p523
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area7530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Leiomodin-2 / Cardiac leiomodin / C-LMOD / Leiomodin


Mass: 4669.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMOD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6P5Q4
#2: Protein/peptide Tropomyosin alpha-1 chain chimeric peptide / Alpha-tropomyosin / Tropomyosin-1


Mass: 3909.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPM1, C15orf13, TMSA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09493

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
113isotropic12D 1H-15N HSQC
121isotropic22D 1H-15N HSQC
132isotropic22D 1H-15N HSQC
151isotropic22D 1H-13C HSQC aliphatic
161isotropic22D 1H-13C HSQC aromatic
171isotropic23D HNCO
181isotropic23D HN(CO)CA
191isotropic23D HNCA
1101isotropic23D CBCA(CO)NH
1111isotropic23D HBHA(CO)NH
1121isotropic23D (H)CCH-TOCSY
1131isotropic23D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY
1152isotropic23D HNCO
1162isotropic23D HN(CO)CA
1172isotropic23D HNCA
1182isotropic23D CBCA(CO)NH
1202isotropic23D (H)CCH-TOCSY
1212isotropic23D HN(CA)CB
1222isotropic12D 1H-15N HSQC
1232isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] leiomodin peptide, 1 mM tropomyosin peptide, 90% H2O/10% D2O15N13C_Lmod2s1_Tpm1a90% H2O/10% D2O
solution20.5 mM [U-13C; U-15N] tropomyosin peptide, 1 mM leiomodin peptide, 90% H2O/10% D2O15N13C_Tpm1a_Lmod2s190% H2O/10% D2O
solution30.3 mM [U-15N] leiomodin peptide, 0.6 mM tropomyosin peptide, 90% H2O/10% D2O15N_Lmod2s1_Tpm1a90% H2O/10% D2O
solution40.3 mM [U-15N] tropomyosin peptide, 0.6 mM leiomodin peptide, 90% H2O/10% D2O15N_Tpm1a_Lmod2s190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMleiomodin peptide[U-13C; U-15N]1
1 mMtropomyosin peptidenatural abundance1
0.5 mMtropomyosin peptide[U-13C; U-15N]2
1 mMleiomodin peptidenatural abundance2
0.3 mMleiomodin peptide[U-15N]3
0.6 mMtropomyosin peptidenatural abundance3
0.3 mMtropomyosin peptide[U-15N]4
0.6 mMleiomodin peptidenatural abundance4
Sample conditionsDetails: 50 mM sodium phosphate; 0.01% sodium azide; 0.2 mM ethylenediaminetetraacetate; 1x cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail (Roche)
Ionic strength: 0.081 M / Ionic strength err: 0.002 / Label: conditions_1 / pH: 6.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
TALOSTALOS+Cornilescu, Delaglio and Baxstructure calculation
NMRViewNMRViewJ Version 9.2.0-b4 with Java 1.8.0_92 x86_64Johnson, One Moon Scientificchemical shift assignment
NMRViewNMRViewJ Version 9.2.0-b4 with Java 1.8.0_92 x86_64Johnson, One Moon Scientificpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 20 / Conformers submitted total number: 10

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