12RT | pdb_000012rt

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

PDB DOI: https://doi.org/10.2210/pdb12RT/pdb
EM Map EMD-76716: 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: 3.96 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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: 203.34 kDa
Atom Count: 13,708
Modeled Residue Count: 1,734
Deposited Residue Count: 1,802
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68369
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ERD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth C]	E [auth A], I [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth C]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain G [auth B] MOL2 format, chain K [auth D] MOL2 format, chain G [auth B] mmCIF format, chain K [auth D] mmCIF format, chain G [auth B]	G [auth B], K [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Focus chain K [auth D] Interactions & Density Focus chain G [auth B] Focus chain K [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]