12RU | pdb_000012ru

In situ cryo-EM structure of axonal microtubules from ghost neurons (expanded lattice)

• PDB DOI: https://doi.org/10.2210/pdb12RU/pdb
• EM Map EMD-76717: 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)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 203.29 kDa 
• Atom Count: 13,706 
• Modeled Residue Count: 1,734 
• Deposited Residue Count: 1,802 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1A chain	A, C	451	Mus musculus	Mutation(s): 0  EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P68369 (Mus musculus) Explore P68369  Go to UniProtKB:  P68369
IMPC:  MGI:98869

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-3 chain	B, D	450	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9ERD7 (Mus musculus) Explore Q9ERD7  Go to UniProtKB:  Q9ERD7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A], H [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	G [auth B], J [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.66 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0_5936
RECONSTRUCTION	cryoSPARC	4.7.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-26 
Deposition Author(s): Bodakuntla, S., Marelli, J., Vasquez-Montes, V., Biertumpfel, C., Mizuno, N.

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

Revision History  

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