8IXB: Tubulin alpha-1A chain

GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin seam region. Determined by electron microscopy at 4.2 Å resolution. Released 16 Aug 2023.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Mus musculus, Homo sapiens
Chains: 12
Atoms: 37,372
Mol. weight: 581.76 kDa
Ligands: ATP, G2P, GTP
Released: 16 Aug 2023

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

Secondary structure: helices and β-sheets

8IXB contains 237 α-helices and 231 β-strands across 12 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: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
α-helix	10-27	18
α-helix	54-57	4
β-strand	59-61	3	18
β-strand	67-69	3	18
β-strand	71-74	4	17
α-helix	81-85	5
β-strand	98	1	17
α-helix	109-110	2
α-helix	111-115	5
α-helix	116-133	18
β-strand	138-145	8	17
α-helix	151-166	16
β-strand	171-178	8	17
α-helix	179-180	2
α-helix	189-203	15
β-strand	206-211	6	17
α-helix	212-221	10
α-helix	230-244	15
α-helix	246-249	4
β-strand	254	1	19
α-helix	260-263	4
β-strand	275-279	5	20
α-helix	284-289	6
α-helix	291-292	2
α-helix	294-301	8
α-helix	304-306	3
β-strand	307	1	20
α-helix	313-315	3
β-strand	318-327	10	20
α-helix	331-343	13
β-strand	349	1	20
β-strand	357-360	4	20
β-strand	361	1	19
α-helix	375-376	2
β-strand	379-387	9	20
α-helix	391-406	16
α-helix	412-417	6
α-helix	421-441	21

Chain E: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	34
α-helix	10-27	18
α-helix	54-57	4
β-strand	59-61	3	35
β-strand	67-69	3	35
β-strand	71-74	4	34
α-helix	81-85	5
β-strand	98	1	34
α-helix	109-110	2
α-helix	111-115	5
α-helix	116-133	18
β-strand	138-145	8	34
α-helix	151-166	16
β-strand	171-178	8	34
α-helix	179-180	2
α-helix	189-203	15
β-strand	206-211	6	34
α-helix	212-218	7
α-helix	219-223	5
α-helix	230-244	15
α-helix	246-249	4
β-strand	254	1	36
α-helix	260-263	4
β-strand	275-279	5	37
α-helix	284-289	6
α-helix	294-301	8
α-helix	304-306	3
β-strand	307	1	37
α-helix	313-315	3
β-strand	318-327	10	37
α-helix	331-343	13
β-strand	349	1	37
β-strand	357-360	4	37
β-strand	361	1	36
α-helix	375-376	2
β-strand	379-387	9	37
α-helix	391-407	17
α-helix	412-417	6
α-helix	421-442	22

Chain F: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	50
α-helix	10-27	18
α-helix	54-57	4
β-strand	59-61	3	51
β-strand	67-69	3	51
β-strand	71-74	4	50
α-helix	81-85	5
β-strand	98	1	50
α-helix	109-110	2
α-helix	111-115	5
α-helix	116-133	18
β-strand	138-145	8	50
α-helix	151-164	14
β-strand	171-178	8	50
α-helix	179-180	2
α-helix	189-203	15
β-strand	206-211	6	50
α-helix	212-221	10
α-helix	230-244	15
α-helix	246-249	4
β-strand	254	1	52
α-helix	260-263	4
β-strand	275-279	5	53
α-helix	284-288	5
α-helix	294-301	8
α-helix	304-306	3
β-strand	307	1	53
α-helix	313-315	3
β-strand	318-327	10	53
α-helix	331-343	13
β-strand	349	1	53
β-strand	357-360	4	53
β-strand	361	1	52
α-helix	375-376	2
β-strand	379-387	9	53
α-helix	391-406	16
α-helix	412-417	6
α-helix	421-441	21

Chain g: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	28
α-helix	9	1
β-strand	10-14	5	29
α-helix	20-25	6
β-strand	32-34	3	30
β-strand	38-40	3	30
β-strand	45-47	3	30
β-strand	51-52	2	29
α-helix	58-65	8
α-helix	68-75	8
β-strand	78-84	7	29
α-helix	91-95	5
β-strand	97	1	31
β-strand	105	1	31
α-helix	108-121	14
β-strand	126-137	12	29
β-strand	142-144	3	29
β-strand	154-157	4	32
β-strand	163-166	4	32
β-strand	171-173	3	29
α-helix	176-189	14
β-strand	193	1	33
β-strand	201	1	33
β-strand	206-216	11	29
β-strand	221-225	5	29
β-strand	227-231	5	29
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	294-301	8	29
α-helix	309-323	15
β-strand	326-327	2	28

Chain H: 23 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
α-helix	54-57	4
β-strand	59-61	3	2
β-strand	67-69	3	2
β-strand	71-74	4	1
α-helix	81-85	5
β-strand	98	1	1
α-helix	109-110	2
α-helix	111-115	5
α-helix	116-133	18
β-strand	138-146	9	1
α-helix	151-166	16
β-strand	171-178	8	1
α-helix	179-180	2
α-helix	189-203	15
β-strand	206-211	6	1
α-helix	212-221	10
α-helix	230-244	15
α-helix	246-249	4
β-strand	254	1	3
α-helix	260-263	4
β-strand	275-279	5	4
α-helix	284-289	6
α-helix	291-292	2
α-helix	294-301	8
α-helix	304-306	3
β-strand	307	1	4
α-helix	313-315	3
β-strand	318-327	10	4
α-helix	331-343	13
β-strand	349	1	4
β-strand	357-360	4	4
β-strand	361	1	3
α-helix	375-376	2
β-strand	379-387	9	4
α-helix	391-407	17
α-helix	412-417	6
α-helix	421-442	22

Chain k: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	44
α-helix	9	1
β-strand	10-14	5	45
α-helix	20-25	6
β-strand	32-34	3	46
β-strand	38-40	3	46
β-strand	45-47	3	46
β-strand	51-52	2	45
α-helix	58-65	8
α-helix	67-75	9
β-strand	78-84	7	45
α-helix	91-95	5
β-strand	97	1	47
β-strand	105	1	47
α-helix	108-121	14
β-strand	126-137	12	45
β-strand	142-144	3	45
β-strand	154-157	4	48
β-strand	163-166	4	48
β-strand	171-173	3	45
α-helix	176-189	14
β-strand	193	1	49
β-strand	201	1	49
β-strand	206-216	11	45
β-strand	221-231	11	45
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	294-301	8	45
α-helix	306-308	3
α-helix	309-323	15
β-strand	326-327	2	44

Chain l: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	11
α-helix	9	1
β-strand	10-14	5	12
α-helix	20-25	6
β-strand	32-34	3	13
β-strand	38-40	3	13
β-strand	45-47	3	13
β-strand	51-52	2	12
α-helix	58-65	8
α-helix	68-75	8
β-strand	78-84	7	12
α-helix	91-95	5
β-strand	97	1	14
β-strand	105	1	14
α-helix	108-121	14
β-strand	126-137	12	12
β-strand	142-144	3	12
β-strand	155-157	3	15
β-strand	163-165	3	15
β-strand	171-173	3	12
α-helix	176-189	14
β-strand	193	1	16
β-strand	201	1	16
β-strand	206-216	11	12
β-strand	221-225	5	12
β-strand	227-231	5	12
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	294-301	8	12
α-helix	306-308	3
α-helix	309-323	15
β-strand	326-327	2	11

Chain m: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-8	2	61
α-helix	9	1
β-strand	10-14	5	62
α-helix	20-25	6
β-strand	32-34	3	63
β-strand	38-40	3	63
β-strand	45-47	3	63
β-strand	51-52	2	62
α-helix	58-65	8
α-helix	68-75	8
β-strand	78-84	7	62
α-helix	91-95	5
β-strand	97	1	64
β-strand	105	1	64
α-helix	108-121	14
β-strand	126-137	12	62
β-strand	142-144	3	62
β-strand	154-157	4	65
β-strand	163-166	4	65
β-strand	171-172	2	62
α-helix	176-188	13
β-strand	193	1	66
β-strand	201	1	66
β-strand	206-216	11	62
β-strand	221-225	5	62
β-strand	227-231	5	62
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	294-301	8	62
α-helix	306-308	3
α-helix	309-323	15
β-strand	326-327	2	61

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1A chain	A, E, F, H	protein	457	Mus musculus	P68369 (AlphaFold model)
Tubulin beta-2A chain	Q, U, V, W	protein	457	Mus musculus	Q7TMM9 (AlphaFold model)
Kinesin-1 heavy chain	g, k, l, m	protein	372	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A, E, F, H), FASTA

>8IXB_1 Tubulin alpha-1A chain (chains A, E, F, H)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIHHHHHHGGGDDSFNTFFS
ETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEI
IDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPA
PQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQI
VSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNA
CFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVG
INYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGME
EGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (Q, U, V, W), FASTA

>8IXB_2 Tubulin beta-2A chain (chains Q, U, V, W)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEAGGSGGDYKDDDK

Sequence of entity 3 (g, k, l, m), FASTA

>8IXB_3 Kinesin-1 heavy chain (chains g, k, l, m)
MGSSHHHHHHSSGLVPRGSHMASMADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGED
TVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEG
KLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHE
DKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENT
QTEQKLSGKLYLVDLAGSAKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPY
RDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTA
EQWKKKYEKEKE

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	4
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4

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 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
12RT 3.96 Å, In situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice)
8IXA 4.2 Å, GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin non-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

Browse structure collections

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