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- PDB-9go5: CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution. -

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Basic information

Entry
Database: PDB / ID: 9go5
TitleCryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution.
ComponentsActin
KeywordsPROTEIN FIBRIL / Fibre / polymer / helical protein / motility
Function / homology
Function and homology information


cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / RHOB GTPase cycle / RHOA GTPase cycle / vacuole inheritance / ascospore wall assembly / actin cortical patch / Swr1 complex / Ino80 complex / actin filament bundle ...cellular bud neck contractile ring / mitotic actomyosin contractile ring contraction / RHOB GTPase cycle / RHOA GTPase cycle / 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 / actin cytoskeleton / chromatin remodeling / DNA repair / DNA-templated transcription / regulation of DNA-templated transcription / chromatin / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus
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 cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBullough, P.A. / Ayscough, K.R. / Lahiri, I. / Tzokov, S.B. / Stevenson, S.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Structure / Year: 2025
Title: Cryo-EM reconstruction of yeast ADP-actin filament at 2.5 Å resolution. A comparison with vertebrate F-actin.
Authors: Sarah R Stevenson / Svetomir B Tzokov / Indrajit Lahiri / Kathryn R Ayscough / Per A Bullough /
Abstract: The core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerizes into filaments (F-actin). Budding yeast possesses a single actin that shares 87%-89% ...The core component of the actin cytoskeleton is the globular protein G-actin, which reversibly polymerizes into filaments (F-actin). Budding yeast possesses a single actin that shares 87%-89% sequence identity with vertebrate actin isoforms. Previous structural studies indicate very close overlap of main-chain backbones. Intriguingly, however, substitution of yeast ACT1 with vertebrate β-cytoplasmic actin severely disrupts cell function and the substitution with a skeletal muscle isoform is lethal. Here we report a 2.5 Å structure of budding yeast F-actin. Previously unresolved side-chain information allows us to highlight four main differences in the comparison of yeast and vertebrate ADP F-actins: a more open nucleotide binding pocket; a more solvent exposed C-terminus; a rearrangement of inter-subunit binding interactions in the vicinity of the D loop and changes in the hydrogen bonding network in the vicinity of histidine 73 (yeast actin) and methyl-histidine 73 (vertebrate actin).
History
DepositionSep 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)210,93515
Polymers208,6785
Non-polymers2,25810
Water6,305350
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


Mass: 41735.547 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ACT1, ABY1, END7, YFL039C / Production host: Komagataella pastoris (fungus)
References: UniProt: P60010, 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Polymer of actin subunits / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 8 / Details: 50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM Tris
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen 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: 2400 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 27 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -167.2 ° / Axial rise/subunit: 2.76 Å / Axial symmetry: C1
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1368572 / Symmetry type: HELICAL
Atomic model buildingMethod: real space / Protocol: AB INITIO MODEL / Space: REAL

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