5W3H: Yeast microtubule stabilized with epothilone

Yeast microtubule stabilized with epothilone. 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: 6,876
Mol. weight: 102.31 kDa
Ligands: EP, GDP, MG, GTP
Released: 19 Jul 2017

Explore 5W3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W3H contains 51 α-helices and 38 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: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	47-50	4
β-strand	55-56	2	3
α-helix	58-60	3
β-strand	61	1	2
β-strand	62-63	2	3
β-strand	66-70	5	1
α-helix	73-80	8
α-helix	83-86	4
α-helix	90-92	3
β-strand	93-95	3	1
α-helix	104-109	6
α-helix	111-129	19
β-strand	133-141	9	1
α-helix	146-150	5
α-helix	151-161	11
β-strand	166-173	8	1
α-helix	174-175	2
α-helix	184-198	15
β-strand	201-206	6	1
α-helix	207-216	10
α-helix	225-244	20
β-strand	247-249	3	4
α-helix	253-260	8
β-strand	270-273	4	4
β-strand	278	1	5
α-helix	282-284	3
α-helix	289-297	9
α-helix	299-301	3
β-strand	302	1	4
α-helix	308-310	3
β-strand	313-322	10	4
α-helix	326-339	14
β-strand	344	1	4
β-strand	352-357	6	4
β-strand	369	1	5
β-strand	374-382	9	4
α-helix	383-385	3
α-helix	386-401	16
α-helix	406-410	5
α-helix	416-439	24

Chain B: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-28	19
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-45	5
α-helix	46-48	3
β-strand	51-53	3	9
α-helix	55-57	3
β-strand	58	1	8
β-strand	59-61	3	9
β-strand	63-67	5	6
α-helix	70-78	9
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-111	3
α-helix	114-125	12
β-strand	130-138	9	6
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	6
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-203	6	6
α-helix	204-213	10
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	10
α-helix	278-281	4
α-helix	286-294	9
α-helix	296-298	3
β-strand	299	1	10
β-strand	310-319	10	10
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	10
β-strand	349-354	6	10
α-helix	357-358	2
β-strand	363-371	9	10
α-helix	372-374	3
α-helix	375-391	17
α-helix	395-399	5
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

>5W3H_1 Tubulin alpha-1 chain (chains A)
MREVISINVGQAGCQIGNACWELYSLEHGIKPDGHLEDGLSKPKGGEEGFSTFFHETGYG
KFVPRAIYVDLEPNVIDEVRNGPYKDLFHPEQLISGKEDAANNYARGHYTVGREILGDVL
DRIRKLADQCDGLQGFLFTHSLGGGTGSGLGSLLLEELSAEYGKKSKLEFAVYPAPQVST
SVVEPYNTVLTTHTTLEHADCTFMVDNEAIYDMCKRNLDIPRPSFANLNNLIAQVVSSVT
ASLRFDGSLNVDLNEFQTNLVPYPRIHFPLVSYSPVLSKSKAFHESNSVSEITNACFEPG
NQMVKCDPRDGKYMATCLLYRGDVVTRDVQRAVEQVKNKKTVQLVDWCPTGFKIGICYEP
PTATPNSQLATVDRAVCMLSNTTSIAEAWKRIDRKFDLMYAKRAFVHWYVGEGMEEGEFT
EAREDLAALERDYIEVGADSYAEEEEF

Sequence of entity 2 (B), FASTA

>5W3H_2 Tubulin beta chain (chains B)
MREIIHISTGQCGNQIGAAFWETICGEHGLDFNGTYHGHDDIQKERLNVYFNEASSGKWV
PRSINVDLEPGTIDAVRNSAIGNLFRPDNYIFGQSSAGNVWAKGHYTEGAELVDSVMDVI
RREAEGCDSLQGFQITHSLGGGTGSGMGTLLISKIREEFPDRMMATFSVLPSPKTSDTVV
EPYNATLSVHQLVEHSDETFCIDNEALYDICQRTLKLNQPSYGDLNNLVSSVMSGVTTSL
RYPGQLNSDLRKLAVNLVPFPRLHFFMVGYAPLTAIGSQSFRSLTVPELTQQMFDAKNMM
AAADPRNGRYLTVAAFFRGKVSVKEVEDEMHKVQSKNSDYFVEWIPNNVQTAVCSVAPQG
LDMAATFIANSTSIQELFKRVGDQFSAMFKRKAFLHWYTSEGMDELEFSEAESNMNDLVS
EYQQYQEATVEDDEEVDENGDFGAPQNQDEPITENFE

Ligands and cofactors

ID	Name	Formula	Copies
EP	Epothilone a	C26 H39 N O6 S	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	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
5W3J 4.0 Å, Yeast microtubule stabilized with Taxol assembled from mutated tubulin
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…

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