9GO5 | pdb_00009go5

CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution.

PDB DOI: https://doi.org/10.2210/pdb9GO5/pdb
EM Map EMD-51491: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Saccharomyces cerevisiae
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2024-09-04 Released: 2025-01-22
Deposition Author(s): Bullough, P.A., Ayscough, K.R., Lahiri, I., Tzokov, S.B., Stevenson, S.R.
Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM reconstruction of yeast ADP-actin filament at 2.5 angstrom resolution. A comparison with vertebrate F-actin.

Stevenson, S.R., Tzokov, S.B., Lahiri, I., Ayscough, K.R., Bullough, P.A.

(2025) Structure 33: 435-442.e3

PubMed: 39798573 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2024.12.008
Primary Citation of Related Structures:
9GO5

PubMed 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% 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).

Organizational Affiliation

Molecular and Cell Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK.

Macromolecule Content

Total Structure Weight: 210.94 kDa
Atom Count: 14,930
Modelled Residue Count: 1,850
Deposited Residue Count: 1,875
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin	A, B, C, D, E	375	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: ACT1, ABY1, END7, YFL039C EC: 3.6.4
UniProt
Find proteins for P60010 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P60010 Go to UniProtKB: P60010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60010
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain N [auth E] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain N [auth E] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain N [auth E]	F [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain O [auth E] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]