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- PDB-2vik: REFINED STRUCTURE OF THE ACTIN-SEVERING DOMAIN VILLIN 14T, DETERM... -

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Entry
Database: PDB / ID: 2vik
TitleREFINED STRUCTURE OF THE ACTIN-SEVERING DOMAIN VILLIN 14T, DETERMINED BY SOLUTION NMR, MINIMIZED AVERAGE STRUCTURE
ComponentsVILLIN 14T
KeywordsACTIN-BINDING PROTEIN / CAPPING PROTEIN / CALCIUM-BINDING PROTEIN / CYTOSKELETAL PROTEIN
Function / homology
Function and homology information


regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping ...regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / 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 / response to bacterium / filopodium / epidermal growth factor receptor signaling pathway / actin filament binding / regulation of cell shape / lamellipodium / actin cytoskeleton / 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 / Severin / Severin ...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 / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / distance geometry
AuthorsMarkus, M.A. / Matsudaira, P. / Wagner, G.
Citation
Journal: Protein Sci. / Year: 1997
Title: Refined structure of villin 14T and a detailed comparison with other actin-severing domains.
Authors: Markus, M.A. / Matsudaira, P. / Wagner, G.
#1: Journal: Biochemistry / Year: 1996
Title: Local Mobility within Villin 14T Probed Via Heteronuclear Relaxation Measurements and a Reduced Spectral Density Mapping
Authors: Markus, M.A. / Dayie, K.T. / Matsudaira, P. / Wagner, G.
#2: Journal: Protein Sci. / Year: 1994
Title: Solution Structure of Villin 14T, a Domain Conserved Among Actin-Severing Proteins
Authors: Markus, M.A. / Nakayama, T. / Matsudaira, P. / Wagner, G.
#3: Journal: J.Biomol.NMR / Year: 1994
Title: 1H, 15N, 13C and 13Co Resonance Assignments and Secondary Structure of Villin 14T, a Domain Conserved Among Actin-Severing Proteins
Authors: Markus, M.A. / Nakayama, T. / Matsudaira, P. / Wagner, G.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 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

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Assembly

Deposited unit
A: VILLIN 14T


Theoretical massNumber of molelcules
Total (without water)14,1751
Polymers14,1751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 20NOE VIOLATIONS < 0.5 A DIHEDRAL VIOL < 5 DEGREES
Representative

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Components

#1: Protein VILLIN 14T / VILLIN DOMAIN 1 / VILLIN SEGMENT 1


Mass: 14174.928 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EPITHELIAL CELLS / Cell line: BL21 / Gene: T7 / Organ: INTESTINE / Plasmid: PAED4, BASED ON T7 PROMOTER / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 4.15 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AMXBrukerAMX6002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DGIIstructure solution
IN INSIGHT IIIIstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
NMR ensembleConformer selection criteria: NOE VIOLATIONS < 0.5 A DIHEDRAL VIOL < 5 DEGREES
Conformers calculated total number: 20 / Conformers submitted total number: 1

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