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- PDB-9jus: Structure of villin bound to an actin trimer -

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Basic information

Entry
Database: PDB / ID: 9jus
TitleStructure of villin bound to an actin trimer
Components
  • Actin, alpha skeletal muscle
  • villin
KeywordsSTRUCTURAL PROTEIN / Villin actin nucleus
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'-DIPHOSPHATE / THIOCYANATE ION / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
Paralvinella sulfincola (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRobinson, R.C.
Funding support France, 2items
OrganizationGrant numberCountry
Other privateMoore-Simons GBMF9743
Human Frontier Science Program (HFSP)RGP0028/2018 France
CitationJournal: To Be Published
Title: The structure of a villin-stabilized actin nucleus
Authors: Robinson, R.C.
History
DepositionOct 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
p: Actin, alpha skeletal muscle
f: Actin, alpha skeletal muscle
g: Actin, alpha skeletal muscle
v: villin
P: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
V: villin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,87938
Polymers439,4358
Non-polymers3,44430
Water3,369187
1
p: Actin, alpha skeletal muscle
f: Actin, alpha skeletal muscle
g: Actin, alpha skeletal muscle
v: villin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,42819
Polymers219,7184
Non-polymers1,71115
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16470 Å2
ΔGint-212 kcal/mol
Surface area81300 Å2
MethodPISA
2
P: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
V: villin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,45119
Polymers219,7184
Non-polymers1,73315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-195 kcal/mol
Surface area81800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.137, 102.432, 147.128
Angle α, β, γ (deg.)77.950, 72.590, 65.960
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 2 types, 8 molecules pfgPFGvV

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 6
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
#2: Protein villin


Mass: 93387.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paralvinella sulfincola (invertebrata) / Production host: Paralvinella sulfincola (invertebrata)

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Non-polymers , 6 types, 217 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris propane, pH 6.5 10% PEG 3350 0.2 M KSCN 5 mM CaCl2/MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.92 Å / Num. obs: 133624 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 79.6 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.051 / Rrim(I) all: 0.096 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1232 / Mean I/σ(I) obs: 1 / Num. unique obs: 13218 / CC1/2: 0.534 / Rpim(I) all: 0.756 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FFK,1H1V

3ffk

1h1v


Resolution: 2.7→29.9 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.226 --
Rwork0.196 --
obs-133624 98.3 %
Displacement parametersBiso mean: 106.83 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30161 0 188 187 30536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001931039
X-RAY DIFFRACTIONf_angle_d0.499442005
X-RAY DIFFRACTIONf_chiral_restr0.04214533
X-RAY DIFFRACTIONf_plane_restr0.00345433
X-RAY DIFFRACTIONf_dihedral_angle_d21.444811606
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree: 0.381 / Rfactor Rwork: 0.344

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