12RV | pdb_000012rv

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

PDB DOI: https://doi.org/10.2210/pdb12RV/pdb
EM Map EMD-76718: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Mus musculus
Mutation(s): No

Deposited: 2026-04-15 Released: 2026-08-26
Deposition Author(s): Bodakuntla, S., Marelli, J., Vasquez-Montes, V., Biertumpfel, C., Mizuno, N.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.24 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 12RV

This is version 1.0 of the entry. See complete history.

Literature

Ghost neuron unlocks in situ high-resolution structural mapping of intracellular architecture in neurons

Bodakuntla, S., Marelli, J., Vasquez-Montes, V., Biertumpfel, C., Mizuno, N.

To be published.

Macromolecule Content

Total Structure Weight: 211.24 kDa
Atom Count: 14,701
Modeled Residue Count: 1,865
Deposited Residue Count: 1,875
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, cytoplasmic 1	A, B [auth E], C [auth B], D [auth C], E [auth D]	375	Mus musculus	Mutation(s): 0 EC: 3.6.4
UniProt
Find proteins for P60710 (Mus musculus) Explore P60710 Go to UniProtKB: P60710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60710
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain H [auth E] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain F [auth A] MOL2 format, chain H [auth E] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain F [auth A] mmCIF format, chain H [auth E] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain F [auth A]	F [auth A], H [auth E], J [auth B], L [auth C], N [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth E] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth E] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth E] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth E] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth E] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	G [auth A], I [auth E], K [auth B], M [auth C], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth E] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth E] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, B [auth E], C [auth B], D [auth C], E [auth D]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.24 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.7.0
MODEL REFINEMENT	PHENIX	2.0-5936

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Vasquez-Montes, V.

Biertumpfel, C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	1ZIAHL006264

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.