9PND: Tubulin beta-3 chain

In situ microtubule of EpoB-induced regenerating axons. Determined by electron microscopy at 3.19 Å resolution. Released 12 Nov 2025.

Method: Electron microscopy
Resolution: 3.19 Å
Organism: Mus musculus
Chains: 4
Atoms: 13,778
Mol. weight: 204.36 kDa
Ligands: GTP, EPB, GDP, MG
Released: 12 Nov 2025

Explore 9PND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PND contains 95 α-helices and 64 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	10-28	19
β-strand	53-55	3	10
β-strand	61-63	3	10
β-strand	65-69	5	9
α-helix	72-80	9
α-helix	82-84	3
α-helix	89-91	3
β-strand	92-94	3	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-140	9	9
α-helix	144-160	17
β-strand	165-172	8	9
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-196	6
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	269-273	5	9
α-helix	278-281	4
α-helix	288-296	9
β-strand	312-321	10	9
α-helix	325-337	13
β-strand	343	1	9
β-strand	353-356	4	9
α-helix	358-360	3
α-helix	368-370	3
β-strand	373-381	9	9
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-436	22

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	30	1	2
β-strand	36	1	2
α-helix	47-49	3
β-strand	51-53	3	3
β-strand	59-61	3	3
β-strand	63-67	5	1
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-92	3	1
α-helix	102-104	3
α-helix	110-126	17
β-strand	130-138	9	1
α-helix	143-158	16
β-strand	163-170	8	1
α-helix	181-195	15
β-strand	198-203	6	1
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	4
α-helix	250-257	8
β-strand	265-266	2	1
β-strand	267-271	5	4
α-helix	286-293	8
β-strand	299	1	4
α-helix	305-307	3
β-strand	310-318	9	4
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	4
β-strand	349-354	6	4
β-strand	364-371	8	4
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-400	5
α-helix	405-427	23

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	11
α-helix	10-28	19
α-helix	35-37	3
β-strand	53-55	3	12
β-strand	61-63	3	12
β-strand	65-68	4	11
α-helix	72-80	9
α-helix	82-84	3
β-strand	92-93	2	11
α-helix	105-109	5
α-helix	111-128	18
β-strand	131-140	10	11
α-helix	144-160	17
β-strand	165-172	8	11
α-helix	173-174	2
α-helix	183-189	7
α-helix	191-197	7
β-strand	200-205	6	11
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	13
α-helix	254-257	4
β-strand	269-273	5	13
α-helix	278-282	5
α-helix	288-296	9
β-strand	312-321	10	13
α-helix	325-337	13
β-strand	343	1	13
β-strand	351-356	6	13
α-helix	359-360	2
α-helix	362-363	2
β-strand	373-381	9	13
α-helix	382-384	3
α-helix	385-401	17
α-helix	405-411	7
α-helix	415-436	22

Chain D: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	70-78	9
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	129-136	8	5
β-strand	138	1	5
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	5
α-helix	181-192	12
β-strand	198-203	6	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	8
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	277-280	4
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	8
α-helix	305-307	3
β-strand	310-318	9	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
α-helix	357-358	2
β-strand	364-371	8	8
α-helix	372-374	3
α-helix	375-390	16
α-helix	395-399	5
α-helix	405-426	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-3 chain	B, D	protein	450	Mus musculus	Q9ERD7 (AlphaFold model)
Detyrosinated tubulin alpha-1A chain	A, C	protein	451	Mus musculus	P68369 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>9PND_1 Tubulin beta-3 chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDDEESEAQGPK

Sequence of entity 2 (A, C), FASTA

>9PND_2 Detyrosinated tubulin alpha-1A chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
EPB	7,11-dihydroxy-8,8,10,12,16-pentamethyl-3-[1-methyl-2-(2-methyl-thiazol-4-yl)vi…	C27 H41 N O6 S	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	4

Primary citation

In situ structural mechanism of epothilone-B-induced CNS axon regeneration. Bodakuntla, S., Taira, K., Yamada, Y. et al. Nature (2025) 648:477-487. DOI 10.1038/s41586-025-09654-z · PubMed

Other PDB entries of the same protein (UniProt Q9ERD7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

12RU 3.66 Å, In situ cryo-EM structure of axonal microtubules from ghost neurons (expanded lattice)
12RT 3.96 Å, In situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice)

Browse structure collections

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