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- PDB-1yu5: Crystal Structure of the Headpiece Domain of Chicken Villin -

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Basic information

Entry
Database: PDB / ID: 1yu5
TitleCrystal Structure of the Headpiece Domain of Chicken Villin
ComponentsVillin
KeywordsSTRUCTURAL PROTEIN / alpha helix / 3-10 helix
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 / barbed-end actin filament capping / actin polymerization or 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsMeng, J. / Vardar, D. / Wang, Y. / Guo, H.C. / Head, J.F. / McKnight, C.J.
CitationJournal: Biochemistry / Year: 2005
Title: High-resolution crystal structures of villin headpiece and mutants with reduced f-actin binding activity.
Authors: Meng, J. / Vardar, D. / Wang, Y. / Guo, H.C. / Head, J.F. / McKnight, C.J.
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Villin


Theoretical massNumber of molelcules
Total (without water)7,6121
Polymers7,6121
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.224, 38.034, 52.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Villin


Mass: 7611.663 Da / Num. of mol.: 1 / Fragment: Headpiece
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PVHP10-76 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P02640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M Na,K Phosphate buffer, 100 mM 2-(4-(2-Hydroxyethyl)-1-piperzainyl) ethanesulfonic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C10.9206
SYNCHROTRONNSLS X8C20.9202,0.9050
Detector
IDDetectorDate
1IMAGE PLATEJun 2, 2001
2IMAGE PLATEAug 2, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.92061
20.92021
30.9051
ReflectionResolution: 1.4→20.14 Å / Num. all: 12905 / Num. obs: 12850 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.053 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.49 Å / Mean I/σ(I) obs: 7.6 / Num. unique all: 2119 / Rsym value: 0.288 / % possible all: 100

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD
Starting model: Bromine phased model, with six bromide sites per asymmetric unit

Resolution: 1.4→100 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 523362.96 / Data cutoff low absF: 0 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1025 8 %Random
Rwork0.192 ---
obs0.194 12850 99.6 %-
all-12905 --
Solvent computationSolvent model: Flat model / Bsol: 61.959 Å2 / ksol: 0.421524 e/Å3
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.55 Å20 Å20 Å2
2---1.604 Å20 Å2
3----1.945 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms537 0 0 95 632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.88
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it1.582
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.4-1.490.2271778.40.20619420.0171596100
1.49-1.540.21121350.19121572
1.54-1.640.22611130.19741586
1.64-1.760.22921280.17371588
1.76-1.940.21321070.18621495
1.94-2.220.20191390.18151611
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param

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