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- PDB-2llf: Sixth Gelsolin-like domain of villin in 5 mM CaCl2 -

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Basic information

Entry
Database: PDB / ID: 2llf
TitleSixth Gelsolin-like domain of villin in 5 mM CaCl2
ComponentsVillin-1
KeywordsSTRUCTURAL PROTEIN / actin regulation / beta-core / modular protein / villin / calcium binding
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 / 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 / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPfaff, D.A. / Brockerman, J. / Fedechkin, S. / Burns, L. / Zhang, F. / Mcknight, C. / Smirnov, S.L.
CitationJournal: Biochemistry / Year: 2013
Title: Gelsolin-like activation of villin: calcium sensitivity of the long helix in domain 6.
Authors: Fedechkin, S.O. / Brockerman, J. / Pfaff, D.A. / Burns, L. / Webb, T. / Nelson, A. / Zhang, F. / Sabantsev, A.V. / Melnikov, A.S. / McKnight, C.J. / Smirnov, S.L.
History
DepositionNov 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Derived calculations / Other
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3May 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-1


Theoretical massNumber of molelcules
Total (without water)12,4281
Polymers12,4281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 600target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Villin-1


Mass: 12427.699 Da / Num. of mol.: 1
Fragment: Gelsolin-like 6 domain containing residues 619-725
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VIL1, VIL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02640

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Sixth Gelsolin-like domain of villin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1422D 1H-1H NOESY
1513D HNHA
1613D HNHB
1713D HBHA(CO)NH
1813D 1H-15N TOCSY
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11113D 1H-15N NOESY
11213D (H)CCH-TOCSY
11313D (H)CCH-COSY
1141HN(CA)CO
1151HNCO
11632D 1H-1H TOCSY
11732D 1H-1H NOESY
11812D 1H-13C HSQC
11912D 1H-13C HSQC aliphatic
12012D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
150 M H2O, 5 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM [U-99% 13C; U-99% 15N] D6, 90% H2O/10% D2O90% H2O/10% D2O
250 M H2O, 5 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM D6, 90% H2O/10% D2O90% H2O/10% D2O
355 M [U-2H] D2O, 10 mM [U-2H] DTT, 0.01 % sodium azide, 5 mM Calcium Chloride, 20 mM [U-2H] PIPES, 1 mM D6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 MH2O-11
5 MD2O-2[U-2H]1
10 mMDTT-3[U-2H]1
0.01 %sodium azide-41
5 mMCalcium Chloride-51
20 mMPIPES-6[U-2H]1
1 mMD6-7[U-99% 13C; U-99% 15N]1
50 MH2O-82
5 MD2O-9[U-2H]2
10 mMDTT-10[U-2H]2
0.01 %sodium azide-112
5 mMCalcium Chloride-122
20 mMPIPES-13[U-2H]2
1 mMD6-142
55 MD2O-15[U-2H]3
10 mMDTT-16[U-2H]3
0.01 %sodium azide-173
5 mMCalcium Chloride-183
20 mMPIPES-19[U-2H]3
1 mMD6-203
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7201
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRView5.2.2Johnson, One Moon Scientificpeak picking
NMRPipe5.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
PREDITOR1Berjanskii MV, Neal S, Wishart DSstructure solution
PREDITOR1Berjanskii MV, Neal S, Wishart DSdihedral prediction
PREDITOR1Berjanskii MV, Neal S, Wishart DSgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1056 / NOE intraresidue total count: 339 / NOE long range total count: 239 / NOE medium range total count: 140 / NOE sequential total count: 338 / Protein chi angle constraints total count: 94 / Protein other angle constraints total count: 104 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 104
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 7.15 ° / Maximum upper distance constraint violation: 0.38 Å
NMR ensemble rmsDistance rms dev: 0.0411 Å

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