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- PDB-9gob: Structure of the F-tractin-F-actin complex -

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Basic information

Entry
Database: PDB / ID: 9gob
TitleStructure of the F-tractin-F-actin complex
Components
  • Actin, alpha skeletal muscle
  • Inositol-trisphosphate 3-kinase A
KeywordsCYTOSOLIC PROTEIN / Actin / F-tractin
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
ADENOSINE-5'-DIPHOSPHATE / Inositol-trisphosphate 3-kinase A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Rattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShatskiy, D. / Belyy, A.
Funding support1items
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
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Actin, alpha skeletal muscle
F: Inositol-trisphosphate 3-kinase A
A: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,40216
Polymers213,1456
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 41760.543 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P68135, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein/peptide Inositol-trisphosphate 3-kinase A / Inositol 1 / 4 / 5-trisphosphate 3-kinase A / IP3 3-kinase A / IP3K A / InsP 3-kinase A


Mass: 4342.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P17105, inositol-trisphosphate 3-kinase
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1F-tractin-F-actin complexCOMPLEX#1-#20MULTIPLE SOURCES
2Actin, alpha skeletal muscleCOMPLEX#11NATURAL
3Inositol-trisphosphate 3-kinase ACOMPLEX#21SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265256 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315136
ELECTRON MICROSCOPYf_angle_d0.73220542
ELECTRON MICROSCOPYf_dihedral_angle_d13.195630
ELECTRON MICROSCOPYf_chiral_restr0.0492283
ELECTRON MICROSCOPYf_plane_restr0.0112627

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