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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 extracellular matrix disassembly / positive regulation of norepinephrine uptake / establishment of apical/basal cell polarity / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / positive regulation of norepinephrine uptake / establishment of apical/basal cell polarity / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / microspike assembly / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / cell projection membrane / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / regulation of G0 to G1 transition / Gap junction degradation / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / adherens junction assembly / cell-cell junction assembly / RHOF GTPase cycle / Adherens junctions interactions / positive regulation of podosome assembly / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / podosome / positive regulation of filopodium assembly / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / brush border / microvillus / kinesin binding / actin filament bundle assembly / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / stress fiber / positive regulation of lamellipodium assembly / ruffle / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / filopodium / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinetochore / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway
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

Supplemental images

emd_51662.png

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)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.54 Å/pix.
x 256 pix.
= 395.008 Å		1.54 Å/pix.
x 256 pix.
= 395.008 Å		1.54 Å/pix.
x 256 pix.
= 395.008 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.543 Å
Density

Histogram

Histogram (log scale)
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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Mask #1

Fileemd_51662_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_51662_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51662_half_map_2.map
Projections & Slices
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Histogram

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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
FSC plot (resolution estimation)

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