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- EMDB-43370: Fascin crosslinked F-actin hexagonal bundle element (460 Angstrom box) -

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Basic information

Entry
Database: EMDB / ID: EMD-43370
TitleFascin crosslinked F-actin hexagonal bundle element (460 Angstrom box)
Map dataLocal filtered 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 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-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43370.png

Downloads & links

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Map

FileDownload / File: emd_43370.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 448 pix.
= 461.44 Å		1.03 Å/pix.
x 448 pix.
= 461.44 Å		1.03 Å/pix.
x 448 pix.
= 461.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.008953321 - 0.025740568
Average (Standard dev.)-0.000006495756 (±0.002120346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 461.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43370_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered reconstruction

Fileemd_43370_additional_1.map
AnnotationUnfiltered reconstruction
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_43370_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_43370_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Processingsingle particle reconstruction
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 K2 SUMMIT (4k x 4k) / Average electron dose: 61.26 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3llp


Details: human fascin 1 crystal structure
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8477
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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