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- PDB-1qqv: SOLUTION STRUCTURE OF THE HEADPIECE DOMAIN OF CHICKEN VILLIN -

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Basic information

Entry
Database: PDB / ID: 1qqv
TitleSOLUTION STRUCTURE OF THE HEADPIECE DOMAIN OF CHICKEN VILLIN
ComponentsVILLIN HEADPIECE DOMAINVillin-1
KeywordsSTRUCTURAL PROTEIN / F-ACTIN BINDING DOMAIN / SALT-BRIDGE
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 / barbed-end actin filament capping ...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 / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / 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 Domain; Chain A / Villin headpiece domain / 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 ...Villin Headpiece Domain; Chain A / Villin headpiece domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING
Model type detailsminimized average
AuthorsVardar, D. / Buckley, D.A. / Frank, B.S. / McKnight, C.J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: NMR structure of an F-actin-binding "headpiece" motif from villin.
Authors: Vardar, D. / Buckley, D.A. / Frank, B.S. / McKnight, C.J.
History
DepositionJun 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
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 HEADPIECE DOMAIN


Theoretical massNumber of molelcules
Total (without water)7,6121
Polymers7,6121
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 31no NOE violation > 0.3, no angle violations greater than 5 degrees
RepresentativeModel #10minimized average structure

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Components

#1: Protein VILLIN HEADPIECE DOMAIN / Villin-1


Mass: 7611.663 Da / Num. of mol.: 1 / Fragment: HP67 / Source method: isolated from a natural source / Source: (natural) 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 NOESY
2223D 15N-SEPARATED NOESY
232HNHA
2422D NOESY
252E-COSY
262HNHB
NMR detailsText: The coordinates are the average of the 10 lowest energy structures of the 31 calculated.

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Sample preparation

Details
Solution-IDContents
11 MM HP67, 10 MM PHOSPHATE BUFFER, PH 7.0
21 MM HP67 U-15N , 10 MM PHOSPHATE BUFFER, PH 7.0
31 MM HP67 U-15N,10% 13C, 10 MM PHOSPHATE BUFFER, PH 7.0
41 MM HP67
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1LOW 7.0 AMBIENT 293 K
2LOW 7.0 AMBIENT 293 K
3LOW 7.0 AMBIENT 293 K
4LOW 7.0 AMBIENT 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLORBrungerrefinement
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1
Details: THIS MINIMIZED AVERAGE STRUCTURE BASED ON A TOTAL OF 1219 DISTANCE RESTRAINTS, 1201 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 18 ARE FROM HYDROGEN BONDS. THERE ARE 61 DIHEDRAL ANGLE RESTRAINTS.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: no NOE violation > 0.3, no angle violations greater than 5 degrees
Conformers calculated total number: 31 / Conformers submitted total number: 1

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