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

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Basic information

Entry
Database: PDB / ID: 12rv
TitleIn situ cryo-EM structure of axonal F-actin from ghost neurons
ComponentsActin, cytoplasmic 1
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / neuron / F-actin / axon
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
ADENOSINE-5'-DIPHOSPHATE / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsBodakuntla, S. / Marelli, J. / Vasquez-Montes, V. / Biertumpfel, C. / Mizuno, N.
Funding support United States, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,23615
Polymers208,9785
Non-polymers2,25810
Water19811
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, negative-staining
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin, cytoplasmic 1 / Beta-actin


Mass: 41795.680 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Details: ACTB (major brain actin) / Source: (natural) Mus musculus (house mouse) / Organ: Brain / Plasmid details: Axon / Strain: CD-1 / Tissue: Thalamus
References: UniProt: P60710, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: F-actin, axonal / Type: ORGANELLE OR CELLULAR COMPONENT
Details: from ghost neuron preparation (hyptonic and mechanical treatment) of explant axons from thalamus primary tissue of mouse embryos
Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD-1 / Cellular location: Axon / Organ: Brain / Tissue: Thalamus primary neuron
Buffer solutionpH: 7.2 / Details: Gibco Neurobasal Media (diluted 1:3 to 160 mOsm)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: ghost neurons prepared by hypotonic and mechanical treatment
Specimen supportDetails: coated with poly-L-lysine and laminin / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 303 K / Details: blot force 4, blot time 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54.52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 15 / Num. of real images: 1196 / Details: curated image number
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 11520 / Height: 8184

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
2SerialEMimage acquisition
4cryoSPARC4.7.0CTF correction
7UCSF ChimeraX1.9model fitting
8Coot0.9.8.93model fitting
10cryoSPARC4.7.0initial Euler assignment
11cryoSPARC4.7.0final Euler assignment
12cryoSPARC4.7.0classification
13cryoSPARC4.7.03D reconstruction
14PHENIX2.0-5936model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 166.647 ° / Axial rise/subunit: 27.514 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 99392
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35558 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: iterative rounds of manual building and automated real-space refinement
Atomic model buildingPDB-ID: 8at2

8at2


Pdb chain-ID: all / Accession code: 8at2 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.24 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215031
ELECTRON MICROSCOPYf_angle_d0.5420365
ELECTRON MICROSCOPYf_dihedral_angle_d7.0722090
ELECTRON MICROSCOPYf_chiral_restr0.0412260
ELECTRON MICROSCOPYf_plane_restr0.0042605

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