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- PDB-9jw0: Structure of the N-terminal 3 domains (V1-V3) villin bound to actin -

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Basic information

Entry
Database: PDB / ID: 9jw0
TitleStructure of the N-terminal 3 domains (V1-V3) villin bound to actin
Components
  • Actin, alpha skeletal muscle
  • Villin
KeywordsSTRUCTURAL PROTEIN / Villin Actin
Function / homology
Function and homology information


Striated Muscle Contraction / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin cytoskeleton / hydrolase activity / ATP binding
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesParalvinella sulfincola (invertebrata)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRobinson, R.C.
Funding support United States, France, 2items
OrganizationGrant numberCountry
Other privateMoore-Simons GBMF9743 United States
Human Frontier Science Program (HFSP)RGP0028/2018 France
CitationJournal: To Be Published
Title: Structure of the N-terminal 3 domains (V1-V3) villin bound to actin
Authors: Robinson, R.C.
History
DepositionOct 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Villin
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0478
Polymers87,3402
Non-polymers7086
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-73 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.710, 93.762, 114.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Villin


Mass: 45242.762 Da / Num. of mol.: 1 / Fragment: N-terminal 3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paralvinella sulfincola (invertebrata) / Production host: Escherichia coli (E. coli)
#2: Protein Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ACTA1, ACTA / Production host: Gallus gallus (chicken) / References: UniProt: P68139
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris propane, pH 8.5, 20% PEG 3350, 0.2 M sodium nitrate, 1 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→20 Å / Num. obs: 24117 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.963 / Rrim(I) all: 0.168 / Net I/av σ(I): 7.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.69→2.75 Å / Rmerge(I) obs: 1.283 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1423 / CC1/2: 0.459 / Rpim(I) all: 0.576 / Rrim(I) all: 1.411 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JUS

9jus


Resolution: 2.69→19.9 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 --
Rwork0.203 --
obs-24117 100 %
Displacement parametersBiso mean: 52.97 Å2
Refinement stepCycle: LAST / Resolution: 2.69→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 36 92 5712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185758
X-RAY DIFFRACTIONf_angle_d0.49157794
X-RAY DIFFRACTIONf_chiral_restr0.0416841
X-RAY DIFFRACTIONf_plane_restr0.00381011
X-RAY DIFFRACTIONf_dihedral_angle_d18.372173
LS refinement shellResolution: 2.69→2.79 Å / Rfactor Rfree: 0.303 / Rfactor Rwork: 0.259

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