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- EMDB-51662: Subtomogram average of fascin-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51662
TitleSubtomogram average of fascin-actin complex
Map data
Sample
  • Complex: Purified fascin mixed with purified actin filaments
    • Organelle or cellular component: actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Organelle or cellular component: purified fascin
      • Protein or peptide: Fascin
Keywordsfascin / actin filament / bundling / STRUCTURAL PROTEIN
Function / homology
Function and homology information


microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of norepinephrine uptake / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / cellular response to cytochalasin B / bBAF complex / microspike assembly / npBAF complex ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of norepinephrine uptake / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / cellular response to cytochalasin B / bBAF complex / microspike assembly / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / cell projection membrane / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / protein localization to adherens junction / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / dense body / Cell-extracellular matrix interactions / postsynaptic actin cytoskeleton / Tat protein binding / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of nucleotide-excision repair / regulation of double-strand break repair / adherens junction assembly / cell-cell junction assembly / RHOF GTPase cycle / Adherens junctions interactions / apical protein localization / positive regulation of podosome assembly / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of filopodium assembly / Sensory processing of sound by inner hair cells of the cochlea / podosome / positive regulation of T cell differentiation / regulation of norepinephrine uptake / apical junction complex / transporter regulator activity / positive regulation of double-strand break repair / maintenance of blood-brain barrier / nitric-oxide synthase binding / establishment or maintenance of cell polarity / cortical cytoskeleton / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / microvillus / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / actin filament bundle assembly / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / stress fiber / ruffle / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / DNA Damage Recognition in GG-NER / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adherens junction / actin filament / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / positive regulation of cell differentiation / filopodium / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / kinetochore / B-WICH complex positively regulates rRNA expression / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / tau protein binding / platelet aggregation
Similarity search - Function
Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. ...Fascin / Fascin, metazoans / Fascin domain / Fascin domain / Actin-crosslinking / 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
Actin, cytoplasmic 1 / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 9.0 Å
AuthorsSong X / Corbalan-Garcia S / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: J Struct Biol / Year: 2025
Title: The mechanism underlying fascin-mediated bundling of actin filaments unveiled by cryo-electron tomography.
Authors: Xiyong Song / Jesús Baltanás-Copado / Muniyandi Selvaraj / Shrikant B Kokate / Esa-Pekka Kumpula / Senena Corbalán-García / Juha T Huiskonen /
Abstract: Fascins are crucial actin-binding proteins linked to carcinomas, such as cancer metastasis. Fascins crosslink unipolar actin filaments into linear and rigid parallel bundles, which play essential ...Fascins are crucial actin-binding proteins linked to carcinomas, such as cancer metastasis. Fascins crosslink unipolar actin filaments into linear and rigid parallel bundles, which play essential roles in the formation of filopodia, stereocilia and other membrane protrusions. However, the mechanism of how fascin bundles actin filaments has remained elusive. Here, we studied the organization of reconstituted fascin-actin bundles by cryo-electron tomography and determined the structure of the fascin-actin complex at 9 Å resolution by subtomogram averaging. Consistent with earlier findings, fascin molecules decorate adjacent actin filaments, positioned at regular intervals corresponding to the half-pitch of actin filaments. The fascin-actin complex structure allows us to verify the binding orientation of fascin between the two actin filaments. Fitting of the previously solved fascin crystal structure facilitates the analysis of the interaction surfaces. Our structural models serve as a blueprint to understand the detailed interactions between fascin and actins and provide new insights for the development of drugs targeting fascin proteins.
History
DepositionSep 30, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_51662.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.543 Å
Density
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-1.7836509 - 3.8895774
Average (Standard dev.)0.013034516 (±0.37922302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 395.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Purified fascin mixed with purified actin filaments

EntireName: Purified fascin mixed with purified actin filaments
Components
  • Complex: Purified fascin mixed with purified actin filaments
    • Organelle or cellular component: actin filament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Organelle or cellular component: purified fascin
      • Protein or peptide: Fascin

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Supramolecule #1: Purified fascin mixed with purified actin filaments

SupramoleculeName: Purified fascin mixed with purified actin filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: actin filament

SupramoleculeName: actin filament / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: purified fascin

SupramoleculeName: purified fascin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.78266 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IEHGIVTNWD DMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSGDGV T HTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLEK SY ELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKEI TAL APSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Fascin

MacromoleculeName: Fascin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.573664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTANGTAEAV QIQFGLINCG NKYLTAEAFG FKVNASASSL KKKQIWTLEQ PPDEAGSAAV CLRSHLGRYL AADKDGNVTC EREVPGPDC RFLIVAHDDG RWSLQSEAHR RYFGGTEDRL SCFAQTVSPA EKWSVHIAMH PQVNIYSVTR EEYAHLSARP A DEIAVDRD ...String:
MTANGTAEAV QIQFGLINCG NKYLTAEAFG FKVNASASSL KKKQIWTLEQ PPDEAGSAAV CLRSHLGRYL AADKDGNVTC EREVPGPDC RFLIVAHDDG RWSLQSEAHR RYFGGTEDRL SCFAQTVSPA EKWSVHIAMH PQVNIYSVTR EEYAHLSARP A DEIAVDRD VPWGVDSLIT LAFQDQRYSV QTADHRFLRH DGRLVARPEP ATGYTLEFRS GKVAFRDCEG RYLAPSGPSG TL KAGKATK VGKDELFALE QSCAQVVLQA ANERNVSTRQ GMDLSANQDE ETDQETFQLE IDRDTKKCAF RTHTGEYWTL TAT GGVQST ASSKNASCYF DIEWRDRRIT LRASNGKFVT SKKNGQLAAS VETAGDSELF LMKLINRPII VFRGEHGFIG CRKV TGTLD ANRSSYDVFQ LEFNDGAYNI KDSTGKYWTV GSDSAVTSSG DTPVDFFFEF CDYNKVAIKV GGRYLKGDHA GVLKA SAET VDPASLWEY

UniProtKB: Fascin

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 6535
ExtractionNumber tomograms: 202 / Number images used: 135371 / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: PROJECTION MATCHING

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