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- EMDB-71056: In situ cryo-EM structure of axonal cofilactin filaments from gho... -

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Basic information

Entry
Database: EMDB / ID: EMD-71056
TitleIn situ cryo-EM structure of axonal cofilactin filaments from ghost neurons
Map datamap from local refinement
Sample
  • Organelle or cellular component: Cofilactin, axonal
    • Protein or peptide: F-actin, axonal
    • Protein or peptide: Cofilin-1, axonal
Keywordscytoskeleton / neuron / F-actin / axon / in situ / cofilin / cofilactin / ghost / STRUCTURAL PROTEIN
Function / homology
Function and homology information


neural fold formation / Interaction between L1 and Ankyrins / Cell-extracellular matrix interactions / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / RHOBTB2 GTPase cycle / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping ...neural fold formation / Interaction between L1 and Ankyrins / Cell-extracellular matrix interactions / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / RHOBTB2 GTPase cycle / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / Formation of annular gap junctions / Gap junction degradation / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / regulation of cell morphogenesis / actin filament fragmentation / cellular response to electrical stimulus / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / MAP2K and MAPK activation / positive regulation of actin filament depolymerization / Regulation of CDH1 Function / RHO GTPases activate IQGAPs / negative regulation of actin filament bundle assembly / Recycling pathway of L1 / modification of postsynaptic actin cytoskeleton / positive regulation of embryonic development / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate Formins / negative regulation of cell size / negative regulation of actin filament depolymerization / positive regulation of cell motility / Clathrin-mediated endocytosis / cellular response to cytochalasin B / cell projection organization / actin filament severing / host-mediated activation of viral process / regulation of transepithelial transport / negative regulation of cell adhesion / neural crest cell migration / positive regulation of synaptic plasticity / morphogenesis of a polarized epithelium / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / establishment of spindle localization / regulation of G0 to G1 transition / regulation of dendritic spine morphogenesis / dense body / negative regulation of cell motility / Tat protein binding / actin filament depolymerization / cellular response to interleukin-6 / postsynaptic actin cytoskeleton / podosome / apical protein localization / adherens junction assembly / regulation of double-strand break repair / negative regulation of dendritic spine maintenance / tight junction / regulation of mitotic metaphase/anaphase transition / cellular response to insulin-like growth factor stimulus / positive regulation of T cell differentiation / establishment of cell polarity / cortical actin cytoskeleton / positive regulation of dendritic spine development / apical junction complex / phosphatidylinositol bisphosphate binding / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / positive regulation of proteolysis / transporter regulator activity / cell leading edge / cortical cytoskeleton / positive regulation of double-strand break repair / lamellipodium membrane / negative regulation of cell differentiation / establishment or maintenance of cell polarity / mitotic cytokinesis / nitric-oxide synthase binding / response to amino acid / cellular response to interleukin-1 / brush border / positive regulation of focal adhesion assembly / positive regulation of myoblast differentiation / regulation of synaptic vesicle endocytosis / kinesin binding / positive regulation of lamellipodium assembly / postsynaptic density, intracellular component / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization / stress fiber / cellular response to epidermal growth factor stimulus
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / 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
Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 5.32 Å
AuthorsBodakuntla S / Marelli J / Vasquez-Montes V / Biertumpfel C / Mizuno N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1ZIAHL006264 United States
CitationJournal: To Be Published
Title: Ghost neuron unlocks in situ high-resolution structural mapping of intracellular architecture in neurons
Authors: Bodakuntla S / Marelli J / Vasquez-Montes V / Biertumpfel C / Mizuno N
History
DepositionJun 5, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71056.png

Downloads & links

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Map

FileDownload / File: emd_71056.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap from local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å		0.82 Å/pix.
x 360 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.053345967 - 0.17626041
Average (Standard dev.)0.000985055 (±0.011894159)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71056_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map from local refinement

Fileemd_71056_half_map_1.map
Annotationhalf map from local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map from local refinement

Fileemd_71056_half_map_2.map
Annotationhalf map from local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cofilactin, axonal

EntireName: Cofilactin, axonal
Components
  • Organelle or cellular component: Cofilactin, axonal
    • Protein or peptide: F-actin, axonal
    • Protein or peptide: Cofilin-1, axonal

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Supramolecule #1: Cofilactin, axonal

SupramoleculeName: Cofilactin, axonal / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: from ghost neuron preparation (hyptonic and mechanical treatment) of explant axons from thalamus primary tissue of mouse embryos
Source (natural)Organism: Mus musculus (house mouse) / Organ: Brain / Tissue: Thalamus primary neuron / Location in cell: Axon

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Macromolecule #1: F-actin, axonal

MacromoleculeName: F-actin, axonal / type: protein_or_peptide / ID: 1 / Details: ACTB (major brain actin) / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: Brain / Tissue: Thalamus
SequenceString: MCEEETTALV CDNGSGLCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLK YPIEHGIITN WDDMEKIWHH SFYNELRVAP EEHPTLLTEA PLNPKANREK M TQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD GVTHNVPIYE ...String:
MCEEETTALV CDNGSGLCKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLK YPIEHGIITN WDDMEKIWHH SFYNELRVAP EEHPTLLTEA PLNPKANREK M TQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD GVTHNVPIYE GYALPHAIMR LD LAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EKS YELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVL SGGTT MYPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISK PEYD EAGPSIVHRK CF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Cofilin-1, axonal

MacromoleculeName: Cofilin-1, axonal / type: protein_or_peptide / ID: 2 / Details: CFL!, Cofilin-1, axonal / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse) / Organ: Brain / Tissue: Thalamus
SequenceString:
MASGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYT TFVKMLPDKD CRYALYDATY ETKESKKEDL VFIFWAPENA PLKSKMIYAS S KDAIKKKL TGIKHELQAN CYEEVKDRCT LAEKLGGSAV ISLEGKPL

UniProtKB: Cofilin-1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.2 / Details: Gibco Neurobasal Media (diluted 1:3 to 160 mOsm)
GridModel: Quantifoil R2/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.8000000000000003 kPa / Details: coated with poly-L-lysine and laminin
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 4, blot time 4 s.
Detailsghost neurons prepared by hypotonic and mechanical treatment

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 17 / Average electron dose: 54.52 e/Å2 / Details: curated image number
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
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 reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.383 Å
Applied symmetry - Helical parameters - Δ&Phi: 162.334 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 5.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 2328
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 4142 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6vao


Chain - Chain ID: all / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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