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- PDB-2ppz: NMR solution Structure of the Villin Headpiece Mutant G34L -

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Basic information

Entry
Database: PDB / ID: 2ppz
TitleNMR solution Structure of the Villin Headpiece Mutant G34L
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / small stable core / alpha helical / thermostable / in silico sequence optimization
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 / 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 / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / microvillus / cellular response to epidermal growth factor stimulus / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / 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
AuthorsGronwald, W. / Hohm, T. / Hoffmann, D.
CitationJournal: Bmc Bioinformatics / Year: 2008
Title: Evolutionary Pareto-optimization of stably folding peptides
Authors: Gronwald, W. / Hohm, T. / Hoffmann, D.
History
DepositionMay 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: database_2 / pdbx_entity_src_syn ...database_2 / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The authors state that residue Met1 of the peptide is not from villin but was included to ...SEQUENCE The authors state that residue Met1 of the peptide is not from villin but was included to compare their fragment with the corresponding structure in PDB entry 1VII where Met1 is also included.

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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)4,2521
Polymers4,2521
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Villin-1


Mass: 4252.007 Da / Num. of mol.: 1
Fragment: C-terminal residues of headpiece domain, sequence database residues 792-826
Mutation: G34L / Source method: obtained synthetically
Details: Synthesized on a peptide synthesizer using the FMOC/But strategy.
Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY, 80 ms mixing time
1212D NOESY, 250 ms mixing time

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Sample preparation

DetailsContents: 4.3 mg peptide dissolved in 0.5 ml 90% H2O, 10% D2O (v/v) and 0.1 mM 2,2-dimethyl-2-silapentane sulfonic acid (DSS) for internal referencing
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
AUREMOL1.1Gronwald W. & Kalbitzer H.R.data analysis
XwinNMR3.2Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: torsion angle dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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