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- PDB-9mf9: Backbone alpha-Methylation in the Villin Headpiece Miniprotein: H... -

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Basic information

Entry
Database: PDB / ID: 9mf9
TitleBackbone alpha-Methylation in the Villin Headpiece Miniprotein: HP35 with Calpha-methyl-Ser at Position 15
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / miniprotein / heterogeneous backbone / proteomimetic
Function / homology
Function and homology information


regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / barbed-end actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / barbed-end actin filament capping / actin filament depolymerization / actin filament capping / actin polymerization or depolymerization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to hepatocyte growth factor stimulus / actin filament bundle / microvillus / positive regulation of epithelial cell migration / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / cellular response to epidermal growth factor stimulus / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / lamellipodium / actin cytoskeleton / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing
AuthorsHarmon, T.W. / Lin, Y. / Sutton, R.T. / Osborne, S. / Horne, W.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM149220 United States
CitationJournal: Chembiochem / Year: 2025
Title: Interplay between C alpha Methylation and C alpha Stereochemistry in the Folding Energetics of a Helix-Rich Miniprotein.
Authors: Harmon, T.W. / Lin, Y. / Sutton, R.T. / Osborne, S.W.J. / Seth Horne, W.
History
DepositionDec 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin-1


Theoretical massNumber of molelcules
Total (without water)4,0591
Polymers4,0591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Villin-1


Mass: 4058.702 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H COSY
131isotropic12D 1H-1H NOESY

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Sample preparation

DetailsType: solution
Contents: 0.44 mM Villin-1 headpiece: Met12Nle, Ser15alphaMeSer, 0.15 mM DSS, 90% H2O/10% D2O
Label: sample_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.44 mMVillin-1 headpiece: Met12Nle, Ser15alphaMeSernatural abundance1
0.15 mMDSSnatural abundance1
Sample conditionsIonic strength: 10 mM / Label: conditions_1 / pH: 5 pH* / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leedata analysis
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leepeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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