5W3J: Tubulin alpha-1 chain

Yeast microtubule stabilized with Taxol assembled from mutated tubulin. Determined by electron microscopy at 4.0 Å resolution. Released 19 Jul 2017.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 6,913
Mol. weight: 102.79 kDa
Ligands: MG, TA1, GDP, GTP
Released: 19 Jul 2017

Explore 5W3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W3J contains 40 α-helices and 44 β-strands across 2 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, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
β-strand	31	1	2
β-strand	35	1	2
α-helix	47-50	4
β-strand	54-56	3	3
β-strand	62-64	3	3
β-strand	66-69	4	1
α-helix	73-80	8
α-helix	90-92	3
β-strand	94	1	1
α-helix	106-110	5
α-helix	111-114	4
α-helix	116-128	13
β-strand	133-139	7	1
α-helix	146-150	5
α-helix	151-161	11
β-strand	166-169	4	1
β-strand	172-173	2	4
α-helix	174-175	2
α-helix	186-195	10
β-strand	201-202	2	1
β-strand	205-206	2	4
α-helix	207-212	6
α-helix	213-217	5
α-helix	225-239	15
α-helix	241-244	4
α-helix	253-255	3
β-strand	272-273	2	5
α-helix	289-294	6
α-helix	299-301	3
β-strand	313-315	3	6
β-strand	316-317	2	7
β-strand	318-322	5	5
α-helix	326-337	12
β-strand	352-353	2	7
β-strand	356	1	5
β-strand	374-378	5	5
β-strand	381-382	2	6
α-helix	385-401	17
α-helix	407-410	4
α-helix	418-438	21

Chain B: 18 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	8
α-helix	10-27	18
β-strand	30	1	9
β-strand	36	1	9
α-helix	44-46	3
β-strand	51-53	3	10
β-strand	59-61	3	10
β-strand	64-66	3	8
α-helix	70-77	8
β-strand	91	1	8
α-helix	103-107	5
α-helix	116-126	11
β-strand	130-136	7	8
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-167	5	8
β-strand	169-170	2	11
α-helix	171-172	2
α-helix	181-190	10
β-strand	198-201	4	8
β-strand	202-203	2	11
α-helix	205-211	7
α-helix	222-236	15
α-helix	252-255	4
β-strand	260	1	12
β-strand	263	1	12
β-strand	265-267	3	8
β-strand	269	1	13
β-strand	270-271	2	8
α-helix	286-293	8
β-strand	299	1	13
β-strand	310	1	14
β-strand	312-319	8	8
α-helix	323-336	14
β-strand	341	1	14
β-strand	349-350	2	8
β-strand	353	1	8
β-strand	363-370	8	8
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-426	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1 chain	A	protein	447	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P09733 (AlphaFold model)
Tubulin beta chain	B	protein	457	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02557 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5W3J_1 Tubulin alpha-1 chain (chains A)
MREVISINVGQAGCQIGNACWELYSLEHGIKPDGHLEDGLSKPKGGEEGFSTFFHETGYG
KFVPRAIYVDLEPNVIDEVRNGPYKDLFHPEQLISGKEDAANNYARGHYTVGREILGDVL
DRIRKLADQCDGLQGFLFTHSLGGGTGSGLGSLLLEELSAEYGKKSKLEFAVYPAPQVST
SVVEPYNTVLTTHTTLEHADCTFMVDNEAIYDMCKRNLDIPRPSFANLNNLIAQVVSSVT
ASLRFDGSLNVDLNEFQTNLVPYPRIHFPLVSYSPVLSKSKAFHESNSVSEITNACFEPG
NQMVKCDPRDGKYMATCLLYRGDVVTRDVQRAVEQVKNKKTVQLVDWCPTGFKIGICYEP
PTATPNSQLATVDRAVCMLSNTTSIAEAWKRIDRKFDLMYAKRAFVHWYVGEGMEEGEFT
EAREDLAALERDYIEVGADSYAEEEEF

Sequence of entity 2 (B), FASTA

>5W3J_2 Tubulin beta chain (chains B)
MREIIHISTGQCGNQIGAKFWEVICDEHGLDFNGTYHGHDDIQKERLNVYFNEASSGKWV
PRSINVDLEPGTIDAVRNSAIGNLFRPDNYIFGQSSAGNVWAKGHYTEGAELVDSVMDVI
RREAEGCDSLQGFQITHSLGGGTGSGMGTLLISKIREEFPDRMMATFSVLPSPKTSDTVV
EPYNATLSVHQLVEHSDETFCIDNEALYDICQRTLKLNQPSYGDLNHLVSSVMSGVTTSL
RYPGQLNSDLRKLAVNLVPFPRLHFFMVGFAPLTAIGSQSFRSLTVPELTQQMFDAKNMM
AAADPRNGRYLTVAAFFRGKVSVKEVEDEMHKVQSKNSDYFVEWIPNNVQTAVCSVAPQG
LDMAATFIANSTSIQELFKRVGDQFSAMFKRKAFLHWYTSEGMDELEFSEAESNMNDLVS
EYQQYQEATVEDDEEVDENGDFGAPQNQDEPITENFE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural differences between yeast and mammalian microtubules revealed by cryo-EM. Howes, S.C., Geyer, E.A., LaFrance, B. et al. J Cell Biol (2017) 216:2669-2677. DOI 10.1083/jcb.201612195 · PubMed

Other PDB entries of the same protein (UniProt P09733 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4U3J 2.81 Å, TOG2:alpha/beta-tubulin complex
4FFB 2.88 Å, A TOG:alpha/beta-tubulin Complex Structure Reveals Conformation-Based Mechanisms For a…
5W3F 3.7 Å, Yeast tubulin polymerized with GTP in vitro
5W3H 4.0 Å, Yeast microtubule stabilized with epothilone
8QV0 6.6 Å, Structure of the native microtubule lattice nucleated from the yeast spindle pole body
8QV3 8.2 Å, Structure of the y-Tubulin Small Complex (yTuSC) as part of the native y-Tubulin Ring…
8QV2 9.2 Å, Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at…

Browse structure collections

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