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- EMDB-76718: In situ cryo-EM structure of axonal F-actin from ghost neurons -

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Basic information

Entry
Database: EMDB / ID: EMD-76718
TitleIn situ cryo-EM structure of axonal F-actin from ghost neurons
Map datasharpened map from local refinement
Sample
  • Organelle or cellular component: F-actin, axonal
    • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
Keywordscytoskeleton / neuron / F-actin / axon / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / Formation of annular gap junctions / Gap junction degradation / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / cellular response to electrical stimulus / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) ...Interaction between L1 and Ankyrins / Cell-extracellular matrix interactions / RHOBTB2 GTPase cycle / Formation of annular gap junctions / Gap junction degradation / RHO GTPases Activate WASPs and WAVEs / EPHB-mediated forward signaling / cellular response to electrical stimulus / Adherens junctions interactions / Formation of the dystrophin-glycoprotein complex (DGC) / MAP2K and MAPK activation / Regulation of CDH1 Function / RHO GTPases activate IQGAPs / Recycling pathway of L1 / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate Formins / Clathrin-mediated endocytosis / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / VEGFA-VEGFR2 Pathway / structural constituent of postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Tat protein binding / postsynaptic actin cytoskeleton / podosome / apical protein localization / adherens junction assembly / regulation of double-strand break repair / tight junction / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / apical junction complex / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / cortical cytoskeleton / positive regulation of double-strand break repair / negative regulation of cell differentiation / establishment or maintenance of cell polarity / nitric-oxide synthase binding / brush border / positive regulation of myoblast differentiation / regulation of synaptic vesicle endocytosis / kinesin binding / 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 / calyx of Held / cell motility / nitric-oxide synthase regulator activity / actin filament / positive regulation of cell differentiation / adherens junction / myelin sheath / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic ribonucleoprotein granule / kinetochore / nuclear matrix / cell-cell junction / actin cytoskeleton / nucleosome / lamellipodium / regulation of apoptotic process / cytoskeleton / regulation of cell cycle / chromatin remodeling / membrane raft / ribonucleoprotein complex / axon / focal adhesion / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / synapse / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / glutamatergic synapse / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.24 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
DepositionApr 15, 2026-
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_76718.png

Downloads & links

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Map

FileDownload / File: emd_76718.map.gz / Format: CCP4 / Size: 479.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map from local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 501 pix.
= 412.824 Å		0.82 Å/pix.
x 501 pix.
= 412.824 Å		0.82 Å/pix.
x 501 pix.
= 412.824 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: 0.06
Minimum - Maximum-0.24970974 - 0.5398545
Average (Standard dev.)-0.00021410476 (±0.016076118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin505050
Dimensions501501501
Spacing501501501
CellA=B=C: 412.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_76718_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_76718_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_76718_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 : F-actin, axonal

EntireName: F-actin, axonal
Components
  • Organelle or cellular component: F-actin, axonal
    • Protein or peptide: Actin, cytoplasmic 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: F-actin, axonal

SupramoleculeName: F-actin, axonal / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
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) / Strain: CD-1 / Organ: Brain / Tissue: Thalamus primary neuron / Location in cell: Axon

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Macromolecule #1: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 1 / Details: ACTB (major brain actin) / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD-1 / Organ: Brain / Tissue: Thalamus
Molecular weightTheoretical: 41.79568 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 11 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 15 / Number real images: 1196 / 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 / Cs: 2.7 mm / 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: 27.514 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.647 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 35558
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 99392 / Software - Name: cryoSPARC (ver. 4.7.0)
Startup modelType of model: NONE / Details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8at2


Chain - Chain ID: all / Chain - Source name: PDB / Chain - Initial model type: experimental model
Detailsiterative rounds of manual building and automated real-space refinement
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-12rv:
In situ cryo-EM structure of axonal F-actin from ghost neurons

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