8IXD: Tubulin alpha-1C chain

GMPCPP-Alpha1C/Beta2A-microtubule decorated with kinesin non-seam region. Determined by electron microscopy at 4.4 Å resolution. Released 16 Aug 2023.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Mus musculus, Homo sapiens
Chains: 27
Atoms: 84,096
Mol. weight: 1306.93 kDa
Ligands: ATP, G2P, GTP
Released: 16 Aug 2023

Explore 8IXD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8IXD contains 495 α-helices and 540 β-strands across 27 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.

Chains a, S, T, U, V, W, X, Y and Z: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	6
β-strand	10-15	6	7
α-helix	20-23	4
β-strand	32-34	3	8
β-strand	38-40	3	8
β-strand	45-47	3	8
β-strand	50-52	3	7
α-helix	58-64	7
α-helix	68-75	8
β-strand	78-84	7	7
α-helix	92-95	4
β-strand	97	1	9
β-strand	105	1	9
α-helix	107-121	15
β-strand	126-129	4	7
β-strand	131-138	8	7
β-strand	141-144	4	7
β-strand	155-157	3	10
β-strand	163-165	3	10
β-strand	171-172	2	7
α-helix	176-188	13
β-strand	192-193	2	11
β-strand	201-202	2	11
β-strand	206-216	11	7
β-strand	222-231	10	7
α-helix	238-241	4
α-helix	246-270	25
α-helix	277-279	3
α-helix	281-285	5
α-helix	287-291	5
β-strand	294-302	9	7
α-helix	306-308	3
α-helix	309-323	15
β-strand	326-327	2	6

Chains A, B, C, D, E, F, G, H and I: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	24
α-helix	10-27	18
β-strand	59-61	3	25
β-strand	67-69	3	25
β-strand	71-75	5	24
α-helix	81-85	5
β-strand	99-100	2	24
α-helix	111-115	5
α-helix	121-133	13
β-strand	138-144	7	24
α-helix	151-155	5
α-helix	156-164	9
β-strand	171-178	8	24
α-helix	179-180	2
α-helix	189-203	15
β-strand	206-211	6	24
α-helix	214-221	8
α-helix	230-244	15
α-helix	246-249	4
β-strand	254	1	26
α-helix	260-263	4
β-strand	268	1	27
β-strand	271	1	27
β-strand	277-279	3	28
α-helix	284-289	6
α-helix	294-301	8
α-helix	304-306	3
β-strand	307	1	28
β-strand	318-327	10	28
α-helix	331-343	13
β-strand	349	1	28
β-strand	359-360	2	28
β-strand	361	1	26
α-helix	365-367	3
α-helix	375-376	2
β-strand	379-387	9	28
α-helix	390-406	17
α-helix	412-417	6
α-helix	421-441	21

Chains J, K, L, M, N, O, P, Q and R: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	29
α-helix	11-28	18
β-strand	30	1	30
β-strand	35	1	31
β-strand	36	1	30
α-helix	42-45	4
β-strand	51-53	3	32
α-helix	55-57	3
β-strand	58	1	31
β-strand	59-61	3	32
β-strand	63-67	5	29
α-helix	71-77	7
β-strand	91-92	2	29
α-helix	101-102	2
α-helix	103-107	5
α-helix	110-126	17
β-strand	130-138	9	29
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	29
α-helix	181-195	15
β-strand	199-203	5	29
α-helix	204-213	10
α-helix	222-236	15
β-strand	246	1	33
α-helix	250-257	8
β-strand	265-266	2	29
β-strand	267-271	5	34
α-helix	286-293	8
β-strand	299	1	34
α-helix	305-307	3
β-strand	310-318	9	34
α-helix	323-335	13
α-helix	338-340	3
β-strand	341	1	34
β-strand	349-352	4	34
β-strand	353	1	33
β-strand	364-371	8	34
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-424	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1C chain	A, B, C, D, E, F, G, H, I	protein	455	Mus musculus	P68373 (AlphaFold model)
Tubulin beta-2A chain	J, K, L, M, N, O, P, Q, R	protein	457	Mus musculus	Q7TMM9 (AlphaFold model)
Kinesin-1 heavy chain	S, T, U, V, W, X, Y, Z, a	protein	372	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I), FASTA

>8IXD_1 Tubulin alpha-1C chain (chains A, B, C, D, E, F, G, H, I)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIHHHHHHGGGDDSFNTFFS
ETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEI
IDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA
PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQI
VSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLTVAEITNA
CFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVG
INYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGME
EGEFSEAREDMAALEKDYEEVGADSAEGDDEGEEY

Sequence of entity 2 (J, K, L, M, N, O, P, Q, R), FASTA

>8IXD_2 Tubulin beta-2A chain (chains J, K, L, M, N, O, P, Q, R)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEAGGSGGDYKDDDK

Sequence of entity 3 (S, T, U, V, W, X, Y, Z, a), FASTA

>8IXD_3 Kinesin-1 heavy chain (chains S, T, U, V, W, X, Y, Z, a)
MGSSHHHHHHSSGLVPRGSHMASMADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGED
TVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG
KLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHE
DKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENT
QTEQKLSGKLYLVDLAGSAKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPY
RDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTA
EQWKKKYEKEKE

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	9
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	9
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	9

Primary citation

Cryo-EM of alpha-tubulin isotype-containing microtubules revealed a contracted structure of alpha 4A/ beta 2A microtubules. Diao, L., Zheng, W., Zhao, Q. et al. Acta Biochim Biophys Sin (Shanghai) (2023) 55:1551-1560. DOI 10.3724/abbs.2023130 · PubMed

Other PDB entries of the same protein (UniProt P68373 (AlphaFold model), which also has an AlphaFold model), best resolution first:

24MC 3.4 Å, Structure of oocyte cytoplasmic lattices
12DL 3.5 Å, Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
8IXE 4.4 Å, GMPCPP-Alpha1C/Beta2A-microtubule decorated with kinesin seam region
9T63 4.7 Å, Asymmetric unit of a cytoplasmic lattice filament repeat unit
9T66 5.3 Å, Complex linking two repeat units of a cytoplasmic lattice filament
9T64 7.3 Å, Cytoplasmic lattice filament repeat unit with the central FBXW-SKP1 complex
9T67 7.7 Å, Cytoplasmic lattice filament repeat unit with ubiquitin
9T68 8.0 Å, Composite structure of the repeat unit of cytoplasmic lattice filament

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