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- EMDB-43372: Subtomogram averaging structure of fascin bound to F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-43372
TitleSubtomogram averaging structure of fascin bound to F-actin
Map dataLocal resolution filtered main map
Sample
  • Complex: Fascin crosslinked F-actin
    • Protein or peptide: Fascin 1
    • Protein or peptide: Alpha actin
KeywordsCytoskeleton / F-actin crosslinker / F-actin bundle / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodsubtomogram averaging / cryo EM / Resolution: 6.7 Å
AuthorsGong R / Reynolds MJ / Alushin GM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141044 United States
Other privateG-2020-14047 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Fascin structural plasticity mediates flexible actin bundle construction.
Authors: Rui Gong / Matthew J Reynolds / Keith R Carney / Keith Hamilton / Tamara C Bidone / Gregory M Alushin /
Abstract: Fascin cross-links actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia and stereocilia. Fascin dysregulation drives aberrant cell migration during ...Fascin cross-links actin filaments (F-actin) into bundles that support tubular membrane protrusions including filopodia and stereocilia. Fascin dysregulation drives aberrant cell migration during metastasis, and fascin inhibitors are under development as cancer therapeutics. Here, we use cryo-EM, cryo-electron tomography coupled with custom denoising and computational modeling to probe human fascin-1's F-actin cross-linking mechanisms across spatial scales. Our fascin cross-bridge structure reveals an asymmetric F-actin binding conformation that is allosterically blocked by the inhibitor G2. Reconstructions of seven-filament hexagonal bundle elements, variability analysis and simulations show how structural plasticity enables fascin to bridge varied interfilament orientations, accommodating mismatches between F-actin's helical symmetry and bundle hexagonal packing. Tomography of many-filament bundles and modeling uncover geometric rules underlying emergent fascin binding patterns, as well as the accumulation of unfavorable cross-links that limit bundle size. Collectively, this work shows how fascin harnesses fine-tuned nanoscale structural dynamics to build and regulate micron-scale F-actin bundles.
History
DepositionJan 14, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43372.png

Downloads & links

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Map

FileDownload / File: emd_43372.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.6 Å/pix.
x 192 pix.
= 499.2 Å		2.6 Å/pix.
x 192 pix.
= 499.2 Å		2.6 Å/pix.
x 192 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 40.0
Minimum - Maximum-74.655820000000006 - 191.712299999999999
Average (Standard dev.)0.0000050765634 (±8.038171)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43372_msk_1.map
Projections & Slices
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Additional map: Sharpened, postprocessed map

Fileemd_43372_additional_1.map
AnnotationSharpened, postprocessed map
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Additional map: Multibody refinement body 2. Postprocessed, masked, sharpened map

Fileemd_43372_additional_2.map
AnnotationMultibody refinement body 2. Postprocessed, masked, sharpened map
Projections & Slices
AxesZYX

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Additional map: Multibody refinement body 1. Postprocessed, masked, sharpened map

Fileemd_43372_additional_3.map
AnnotationMultibody refinement body 1. Postprocessed, masked, sharpened map
Projections & Slices
AxesZYX

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Half map: Half map 2

Fileemd_43372_half_map_1.map
AnnotationHalf map 2
Projections & Slices
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Histogram

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Half map: Half map 1

Fileemd_43372_half_map_2.map
AnnotationHalf map 1
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Sample components

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Entire : Fascin crosslinked F-actin

EntireName: Fascin crosslinked F-actin
Components
  • Complex: Fascin crosslinked F-actin
    • Protein or peptide: Fascin 1
    • Protein or peptide: Alpha actin

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Supramolecule #1: Fascin crosslinked F-actin

SupramoleculeName: Fascin crosslinked F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.4 kDa/nm

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Macromolecule #1: Fascin 1

MacromoleculeName: Fascin 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMTANG TAEAVQIQFG LINCGNKYLT AEAFGFKVNA SASSLKKKQI WTLEQPPDEA GSAAVCLRSH LGRYLAADKD GNVTCEREVP GPDCRFLIVA HDDGRWSLQS EAHRRYFGGT EDRLSCFAQT VSPAEKWSVH IAMHPQVNIY SVTRKRYAHL SARPADEIAV ...String:
GPLGSMTANG TAEAVQIQFG LINCGNKYLT AEAFGFKVNA SASSLKKKQI WTLEQPPDEA GSAAVCLRSH LGRYLAADKD GNVTCEREVP GPDCRFLIVA HDDGRWSLQS EAHRRYFGGT EDRLSCFAQT VSPAEKWSVH IAMHPQVNIY SVTRKRYAHL SARPADEIAV DRDVPWGVDS LITLAFQDQR YSVQTADHRF LRHDGRLVAR PEPATGYTLE FRSGKVAFRD CEGRYLAPSG PSGTLKAGKA TKVGKDELFA LEQSCAQVVL QAANERNVST RQGMDLSANQ DEETDQETFQ LEIDRDTKKC AFRTHTGKYW TLTATGGVQS TASSKNASCY FDIEWRDRRI TLRASNGKFV TSKKNGQLAA SVETAGDSEL FLMKLINRPI IVFRGEHGFI GCRKVTGTLD ANRSSYDVFQ LEFNDGAYNI KDSTGKYWTV GSDSAVTSSG DTPVDFFFEF CDYNKVAIKV GGRYLKGDHA GVLKASAETV DPASLWEY

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Macromolecule #2: Alpha actin

MacromoleculeName: Alpha actin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
SequenceString: DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITNWDDM EKIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN VPIYEGYALP ...String:
DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITNWDDM EKIWHHTFYN ELRVAPEEHP TLLTEAPLNP KANREKMTQI MFETFNVPAM YVAIQAVLSL YASGRTTGIV LDSGDGVTHN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSYEL PDGQVITIGN ERFRCPETLF QPSFIGMESA GIHETTYNSI MKCDIDIRKD LYANNVMSGG TTMYPGIADR MQKEITALAP STMKIKIIAP PERKYSVWIG GSILASLSTF QQMWITKQEY DEAGPSIVHR KCF

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.64 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 26000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 129948
ExtractionNumber tomograms: 26 / Number images used: 134733
Details: Custom picking performed using neural-network-based approach.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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