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- PDB-8r3h: Phalloidin bound F-actin -

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Basic information

Entry
Database: PDB / ID: 8r3h
TitlePhalloidin bound F-actin
Components
  • Actin, alpha skeletal muscle
  • phalloidin
KeywordsCYTOSOLIC PROTEIN / cytoskeleton
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 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesGallus (bird)
Amanita phalloides (death cap)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsYuan, B. / Paraschiakos, T. / Windhorst, S. / Marlovits, T.C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)152/774-1, 152/775-1, 152/776-1 and 152/777-1 Germany
CitationJournal: To Be Published
Title: Phalloidin bound F-actin
Authors: Yuan, B. / Paraschiakos, T. / Windhorst, S. / Marlovits, T.C.
History
DepositionNov 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
X: phalloidin
Y: phalloidin
Z: phalloidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,23418
Polymers212,9778
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 42109.973 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus (bird) / Gene: ACTA1, ACTA / Production host: Gallus (bird)
References: UniProt: P68139, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide phalloidin


Mass: 808.899 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Amanita phalloides (death cap)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Phalloidin bound F-actin / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Gallus (bird)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.75 ° / Axial rise/subunit: 27.78 Å / Axial symmetry: C1
3D reconstructionResolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 128335 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414991
ELECTRON MICROSCOPYf_angle_d0.550620360
ELECTRON MICROSCOPYf_chiral_restr0.04262270
ELECTRON MICROSCOPYf_plane_restr0.00322591
ELECTRON MICROSCOPYf_dihedral_angle_d8.36492086

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