9GOB | pdb_00009gob

Structure of the F-tractin-F-actin complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9GOB

This is version 1.2 of the entry. See complete history

Literature

Structure of the F-tractin-F-actin complex.

Shatskiy, D.Sivan, A.Wedlich-Soldner, R.Belyy, A.

(2025) J Cell Biol 224

  • DOI: https://doi.org/10.1083/jcb.202409192
  • Primary Citation Related Structures: 
    9GOB, 9HM9

  • PubMed Abstract: 

    F-tractin is a peptide widely used to visualize the actin cytoskeleton in live eukaryotic cells but has been reported to impair cell migration and induce actin bundling at high expression levels. To elucidate these effects, we determined the cryo-EM structure of the F-tractin-F-actin complex, revealing that F-tractin consists of a flexible N-terminal region and an amphipathic C-terminal helix. The N-terminal part is dispensable for F-actin binding but responsible for the bundling effect. Based on these insights, we developed an optimized F-tractin, which eliminates the N-terminal region and minimizes bundling while retaining strong actin labeling. The C-terminal helix interacts with a hydrophobic pocket formed by two neighboring actin subunits, an interaction region shared by many actin-binding polypeptides, including the popular actin-binding probe Lifeact. Thus, rather than contrasting F-tractin and Lifeact, our data indicate that these peptides have analogous modes of interaction with F-actin. Our study dissects the structural elements of F-tractin and provides a foundation for developing future actin probes.


  • Organizational Affiliation
    • Membrane Enzymology Group, Groningen Institute of Biomolecular Sciences and Biotechnology (GBB), Faculty of Science and Engineering, University of Groningen , Groningen, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 215.4 kDa 
  • Atom Count: 14,814 
  • Modeled Residue Count: 1,879 
  • Deposited Residue Count: 1,913 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, alpha skeletal muscleA [auth C],
C [auth A],
D [auth E],
E [auth B],
F [auth D]
374Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus)
Explore P68135 
Go to UniProtKB:  P68135
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68135
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Inositol-trisphosphate 3-kinase AB [auth F]43Rattus norvegicusMutation(s): 0 
EC: 2.7.1.127
UniProt
Find proteins for P17105 (Rattus norvegicus)
Explore P17105 
Go to UniProtKB:  P17105
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17105
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
G [auth C],
I [auth A],
K [auth E],
M [auth B],
O [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth C],
J [auth A],
L [auth E],
N [auth B],
P [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A [auth C],
C [auth A],
D [auth E],
E [auth B],
F [auth D]
L-PEPTIDE LINKINGC7 H11 N3 O2HIS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-19
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-02
    Changes: Data collection