12RT: Detyrosinated tubulin alpha-1A chain

In situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice). Determined by electron microscopy at 3.96 Å resolution. Released 26 Aug 2026.

Method: Electron microscopy
Resolution: 3.96 Å
Organism: Mus musculus
Chains: 4
Atoms: 13,708
Mol. weight: 203.34 kDa
Ligands: GDP, MG, GTP
Released: 26 Aug 2026

Explore 12RT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

12RT contains 90 α-helices and 69 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: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	10-27	18
β-strand	35	1	2
β-strand	53-56	4	2
β-strand	60-63	4	2
β-strand	65-69	5	1
α-helix	72-80	9
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	131-140	10	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	3
α-helix	252-258	7
β-strand	262	1	4
β-strand	265	1	4
β-strand	272	1	3
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	351-356	6	3
α-helix	358-360	3
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	384-400	17
α-helix	406-411	6
α-helix	415-436	22

Chain B: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	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	51-53	3	7
β-strand	59-61	3	7
β-strand	63-66	4	5
α-helix	71-78	8
β-strand	90-91	2	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	132-136	5	5
α-helix	142-158	17
β-strand	163-170	8	5
α-helix	181-195	15
β-strand	198-203	6	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	276-281	6
α-helix	286-294	9
α-helix	296-298	3
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	375-390	16
α-helix	396-401	6
α-helix	405-427	23

Chain C: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	10-27	18
β-strand	35	1	10
β-strand	53-56	4	10
β-strand	60-63	4	10
β-strand	65-69	5	9
α-helix	72-80	9
β-strand	93-94	2	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-138	7	9
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	9
α-helix	173-174	2
α-helix	183-196	14
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	262	1	11
β-strand	265	1	11
β-strand	271-272	2	12
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	12
α-helix	325-337	13
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	358-360	3
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	384-400	17
α-helix	406-411	6
α-helix	415-436	22

Chain D: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	13
α-helix	10-27	18
β-strand	30	1	14
β-strand	36	1	14
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-52	2	15
α-helix	53	1
α-helix	55-57	3
β-strand	60-61	2	15
β-strand	63-67	5	13
α-helix	70-78	9
α-helix	87-89	3
β-strand	90-92	3	13
α-helix	103-107	5
α-helix	110-126	17
β-strand	129-136	8	13
β-strand	138	1	16
α-helix	142-158	17
β-strand	163-166	4	13
β-strand	169-170	2	16
α-helix	181-195	15
β-strand	198-200	3	13
β-strand	202-203	2	16
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
β-strand	246	1	17
α-helix	250-257	8
β-strand	265-266	2	13
β-strand	267-271	5	17
α-helix	286-294	9
α-helix	296-298	3
β-strand	310-318	9	17
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	17
β-strand	349-354	6	17
α-helix	357-358	2
β-strand	364-371	8	17
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-401	6
α-helix	405-427	23

Molecules and chains

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

Sequence of entity 1 (A, C), FASTA

>12RT_1 Detyrosinated tubulin alpha-1A chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>12RT_2 Tubulin beta-3 chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDDEESEAQGPK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MG	Magnesium ion	Mg	4
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Ghost neuron unlocks in situ high-resolution structural mapping of intracellular architecture in neurons. Bodakuntla, S., Marelli, J., Vasquez-Montes, V. et al. To be published.

Other PDB entries of the same protein (UniProt P68369 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JZD 2.48 Å, Crystal structure of peptide-bound VASH2-SVBP complex
9PND 3.19 Å, In situ microtubule of EpoB-induced regenerating axons
12RU 3.66 Å, In situ cryo-EM structure of axonal microtubules from ghost neurons (expanded lattice)
9XRL 3.74 Å, Structure of mouse cytoplasmic lattice (CPL) repeating unit
8IXA 4.2 Å, GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin non-seam region
8IXB 4.2 Å, GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region
9SFP 4.2 Å, Native cytoplasmic lattices from mouse oocytes
8TO0 7.7 Å, 48-nm repeating structure of doublets from mouse sperm flagella

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