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- PDB-8thy: Yeast actin A167E mutant rabbit-like -

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Basic information

Entry
Database: PDB / ID: 8thy
TitleYeast actin A167E mutant rabbit-like
ComponentsActin
KeywordsCYTOSOLIC PROTEIN / actin filaments / cytoskeleton / cations / stiffness
Function / homology
Function and homology information


cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / fungal biofilm matrix / vacuole inheritance / ascospore wall assembly / actin cortical patch / Swr1 complex / Ino80 complex / actin filament bundle / establishment of cell polarity ...cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / fungal biofilm matrix / vacuole inheritance / ascospore wall assembly / actin cortical patch / Swr1 complex / Ino80 complex / actin filament bundle / establishment of cell polarity / NuA4 histone acetyltransferase complex / protein secretion / actin filament / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endocytosis / chromatin remodeling / DNA repair / ATP hydrolysis activity / extracellular region / ATP binding / identical protein binding / cytosol
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
Similarity search - Component
Biological speciesSaccharomyces (fungus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsVolkmann, N. / Hanein, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: yeast actin A167E mutant rabbit-like
Authors: Volkmann, N. / Hanein, D.
History
DepositionJul 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Structure summary / Category: em_software / pdbx_entry_details
Item: _em_software.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin
B: Actin
C: Actin
D: Actin
E: Actin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,41715
Polymers206,1605
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin


Mass: 41231.973 Da / Num. of mol.: 5 / Mutation: A167E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces (fungus) / Gene: ACT1, CAGL0K12694g / Production host: Saccharomyces (fungus)
References: UniProt: P60009, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: yeast actin A167E mutant filament / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Saccharomyces (fungus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -167.25 ° / Axial rise/subunit: 27.49 Å / Axial symmetry: C1
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195534 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00514925
ELECTRON MICROSCOPYf_angle_d0.74720235
ELECTRON MICROSCOPYf_dihedral_angle_d13.1935560
ELECTRON MICROSCOPYf_chiral_restr0.0462230
ELECTRON MICROSCOPYf_plane_restr0.0182595

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