9PND | pdb_00009pnd

In situ microtubule of EpoB-induced regenerating axons

PDB DOI: https://doi.org/10.2210/pdb9PND/pdb
EM Map EMD-71750: EMDB EMDataResource

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

Deposited: 2025-07-20 Released: 2025-11-12
Deposition Author(s): Bodakuntla, S., Taira, K., Yamada, Y., Alvarez-Brecht, P., Cada, A.K., Basnet, N., Zhang, R., Martinez-Sanchez, A., 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: 3.19 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

In situ structural mechanism of epothilone-B-induced CNS axon regeneration.

Bodakuntla, S., Taira, K., Yamada, Y., Alvarez-Brecht, P., Cada, A.K., Basnet, N., Zhang, R., Martinez-Sanchez, A., Biertumpfel, C., Mizuno, N.

(2025) Nature 648: 477-487

PubMed: 41224993 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-025-09654-z
Primary Citation Related Structures:
9PND

PubMed Abstract:
Axons in the adult central nervous system (CNS) do not regenerate following injury, in contrast to neurons in the peripheral nervous system and neuronal growth during embryonic development. The molecular mechanisms that prevent regeneration of neurons in the CNS remain largely unknown ^1,2. Here, to address the intracellular response to injury, we developed an in situ cryo-electron tomography and cryo-electron microscopy platform to mimic axonal damage and present the structural mechanism underlying thalamic axon regeneration induced by the drug epothilone B. We observed that stabilized microtubules extend beyond the injury site, generating membrane tension and driving membrane expansion. Cryo-electron microscopy reveals the in situ structure of microtubules at 3.19 Å resolution, which engage epothilone B within the microtubule lattice at the regenerating front. During repair, tubulin clusters are delivered and incorporated into polymerizing microtubules at the regenerating site. These microtubule shoots serve as scaffolds for various types of vesicles and endoplasmic reticulum, facilitating the supply of materials necessary for axon repair until membrane tension normalizes. We demonstrate the unexpected ability of neuronal cells to adjust to strain induced by epothilone B, which creates homeostatic imbalances and activates axons to regeneration mode.

Organizational Affiliation

Laboratory of Structural Cell Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.

Macromolecule Content

Total Structure Weight: 204.36 kDa
Atom Count: 13,778
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
Tubulin beta-3 chain	A [auth B], B [auth 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

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Detyrosinated tubulin alpha-1A chain	C [auth A], D [auth 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth C] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] mmCIF format, chain K [auth A] mmCIF format, chain M [auth C]	K [auth A], M [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain K [auth A] Focus chain M [auth C] Interactions & Density Focus chain K [auth A] Focus chain M [auth C]
EPB (Subject of Investigation/LOI) Query on EPB Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain J [auth D] MOL2 format, chain G [auth B] MOL2 format, chain J [auth D] mmCIF format, chain G [auth B] mmCIF format, chain J [auth D]	G [auth B], J [auth D]	7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE C₂₇ H₄₁ N O₆ S QXRSDHAAWVKZLJ-PVYNADRNSA-N		Interactions Focus chain G [auth B] Focus chain J [auth D] Interactions & Density Focus chain G [auth B] Focus chain J [auth D]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain I [auth D] MOL2 format, chain F [auth B] MOL2 format, chain I [auth D] mmCIF format, chain F [auth B] mmCIF format, chain I [auth D]	F [auth B], I [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth B] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain H [auth D] SDF format, chain L [auth A] SDF format, chain N [auth C] MOL2 format, chain E [auth B] MOL2 format, chain H [auth D] MOL2 format, chain L [auth A] MOL2 format, chain N [auth C] mmCIF format, chain E [auth B] mmCIF format, chain H [auth D] mmCIF format, chain L [auth A] mmCIF format, chain N [auth C]	E [auth B], H [auth D], L [auth A], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain H [auth D] Focus chain L [auth A] Focus chain N [auth C] Interactions & Density Focus chain E [auth B] Focus chain H [auth D] Focus chain L [auth A] Focus chain N [auth C]