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- EMDB-52289: Structure of the optimized F-tractin in complex with F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-52289
TitleStructure of the optimized F-tractin in complex with F-actin
Map data
Sample
  • Complex: Optimized F-tractin in complex with F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Inositol-trisphosphate 3-kinase A
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsActin / F-tractin / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity ...inositol-trisphosphate 3-kinase / Synthesis of IP3 and IP4 in the cytosol / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / modification of postsynaptic actin cytoskeleton / inositol phosphate biosynthetic process / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / troponin I binding / filamentous actin / phosphatidylinositol phosphate biosynthetic process / mesenchyme migration / actin filament bundle / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / cellular response to calcium ion / filopodium / actin filament / regulation of synaptic plasticity / small GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to calcium ion / calcium-dependent protein binding / lamellipodium / cell body / actin cytoskeleton organization / dendritic spine / cytoskeleton / hydrolase activity / calmodulin binding / protein domain specific binding / calcium ion binding / positive regulation of gene expression / glutamatergic synapse / magnesium ion binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / 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
Inositol-trisphosphate 3-kinase A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsShatskiy D / Belyy A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Cell Biol / Year: 2025
Title: Structure of the F-tractin-F-actin complex.
Authors: Dmitry Shatskiy / Athul Sivan / Roland Wedlich-Söldner / Alexander Belyy /
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 ...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.
History
DepositionDec 7, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52289.png

Downloads & links

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Map

FileDownload / File: emd_52289.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.15850617 - 1.2320987
Average (Standard dev.)-0.0011322402 (±0.06861274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52289_msk_1.map
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Additional map: #1

Fileemd_52289_additional_1.map
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Half map: #2

Fileemd_52289_half_map_1.map
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Half map: #1

Fileemd_52289_half_map_2.map
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Sample components

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Entire : Optimized F-tractin in complex with F-actin

EntireName: Optimized F-tractin in complex with F-actin
Components
  • Complex: Optimized F-tractin in complex with F-actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Inositol-trisphosphate 3-kinase A
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Optimized F-tractin in complex with F-actin

SupramoleculeName: Optimized F-tractin in complex with F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 41.760543 KDa
SequenceString: EDETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIIT NWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGD GV THNVPIYEGY ...String:
EDETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIIT NWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGD GV THNVPIYEGY ALPHAIMRLD LAGRDLTDYL MKILTERGYS FVTTAEREIV RDIKEKLCYV ALDFENEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV MSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI TKQEYDEAGP SIVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Inositol-trisphosphate 3-kinase A

MacromoleculeName: Inositol-trisphosphate 3-kinase A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: inositol-trisphosphate 3-kinase
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 2.245585 KDa
SequenceString:
APRRSVGELR LLFEARAASA A

UniProtKB: Inositol-trisphosphate 3-kinase A

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3835

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 298240
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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