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- EMDB-43365: Cryo-EM structure of fascin bound to F-actin (actin binding site 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-43365
TitleCryo-EM structure of fascin bound to F-actin (actin binding site 2)
Map dataLocal resolution filtered map (used for model building)
Sample
  • Complex: Fascin crosslinked F-actin
    • Protein or peptide: Fascin
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCytoskeleton / F-actin crosslinker / F-actin bundle / STRUCTURAL PROTEIN
Function / homology
Function and homology information


microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / Striated Muscle Contraction / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly ...microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / Striated Muscle Contraction / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / podosome / positive regulation of filopodium assembly / establishment or maintenance of cell polarity / microvillus / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / stress fiber / skeletal muscle fiber development / positive regulation of lamellipodium assembly / ruffle / filopodium / actin filament / regulation of actin cytoskeleton organization / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / actin filament binding / cell-cell junction / cell migration / lamellipodium / actin cytoskeleton / actin binding / actin cytoskeleton organization / growth cone / cell cortex / protein-macromolecule adaptor activity / Interleukin-4 and Interleukin-13 signaling / cytoskeleton / hydrolase activity / cadherin binding / RNA binding / extracellular exosome / ATP binding / cytosol / cytoplasm
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, alpha skeletal muscle / Fascin
Similarity search - Component
Biological speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
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_43365.png

Downloads & links

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Map

FileDownload / File: emd_43365.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map (used for model building)
Projections & slices

Image control

Size
Brightness
Contrast
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: 0.02
Minimum - Maximum-0.069368415 - 0.1492841
Average (Standard dev.)0.000009359395 (±0.0023437466)
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_43365_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_43365_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_43365_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_43365_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
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Fascin crosslinked F-actin

SupramoleculeName: Fascin crosslinked F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.4 kDa/nm

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Macromolecule #1: Fascin

MacromoleculeName: Fascin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.013328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMTANG TAEAVQIQFG LINCGNKYLT AEAFGFKVNA SASSLKKKQI WTLEQPPDEA GSAAVCLRSH LGRYLAADKD GNVTCEREV PGPDCRFLIV AHDDGRWSLQ SEAHRRYFGG TEDRLSCFAQ TVSPAEKWSV HIAMHPQVNI YSVTRKRYAH L SARPADEI ...String:
GPLGSMTANG TAEAVQIQFG LINCGNKYLT AEAFGFKVNA SASSLKKKQI WTLEQPPDEA GSAAVCLRSH LGRYLAADKD GNVTCEREV PGPDCRFLIV AHDDGRWSLQ SEAHRRYFGG TEDRLSCFAQ TVSPAEKWSV HIAMHPQVNI YSVTRKRYAH L SARPADEI AVDRDVPWGV DSLITLAFQD QRYSVQTADH RFLRHDGRLV ARPEPATGYT LEFRSGKVAF RDCEGRYLAP SG PSGTLKA GKATKVGKDE LFALEQSCAQ VVLQAANERN VSTRQGMDLS ANQDEETDQE TFQLEIDRDT KKCAFRTHTG KYW TLTATG GVQSTASSKN ASCYFDIEWR DRRITLRASN GKFVTSKKNG QLAASVETAG DSELFLMKLI NRPIIVFRGE HGFI GCRKV TGTLDANRSS YDVFQLEFND GAYNIKDSTG KYWTVGSDSA VTSSGDTPVD FFFEFCDYNK VAIKVGGRYL KGDHA GVLK ASAETVDPAS LWEY

UniProtKB: Fascin

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 41.63143 KDa
SequenceString: DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA ...String:
DETTALVCDN GSGLVKAGFA GDDAPRAVFP SIVGRPRHQG VMVGMGQKDS YVGDEAQSKR GILTLKYPIE (HIC)GIITN WDD MEKIWHHTFY NELRVAPEEH PTLLTEAPLN PKANREKMTQ IMFETFNVPA MYVAIQAVLS LYASGRTTGI VLDSGDG VT HNVPIYEGYA LPHAIMRLDL AGRDLTDYLM KILTERGYSF VTTAEREIVR DIKEKLCYVA LDFENEMATA ASSSSLEK S YELPDGQVIT IGNERFRCPE TLFQPSFIGM ESAGIHETTY NSIMKCDIDI RKDLYANNVM SGGTTMYPGI ADRMQKEIT ALAPSTMKIK IIAPPERKYS VWIGGSILAS LSTFQQMWIT KQEYDEAGPS IVHRKCF

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3llp


Details: human fascin 1 crystal structure
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 113800
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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