5W3F: Yeast tubulin polymerized with GTP in vitro

Yeast tubulin polymerized with GTP in vitro. Determined by electron microscopy at 3.7 Å resolution. Released 19 Jul 2017.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 2
Atoms: 6,842
Mol. weight: 101.81 kDa
Ligands: GDP, GTP, MG
Released: 19 Jul 2017

Explore 5W3F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W3F contains 51 α-helices and 37 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: 30 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
β-strand	54-55	2	2
α-helix	56	1
β-strand	63-64	2	2
β-strand	66-69	4	1
α-helix	73-80	8
α-helix	85-87	3
α-helix	90-92	3
β-strand	93-94	2	1
α-helix	104-105	2
α-helix	106-110	5
α-helix	112-114	3
α-helix	116-129	14
β-strand	135-141	7	1
α-helix	145	1
α-helix	146-150	5
α-helix	151-161	11
β-strand	166-173	8	1
α-helix	174	1
β-strand	175	1	3
β-strand	178	1	3
α-helix	184-198	15
β-strand	201-206	6	1
α-helix	207-216	10
α-helix	225-238	14
α-helix	241-243	3
β-strand	247-249	3	4
α-helix	255-260	6
β-strand	270-274	5	4
β-strand	278	1	5
α-helix	289-297	9
α-helix	299-301	3
β-strand	313	1	6
β-strand	316-322	7	4
α-helix	326-337	12
α-helix	343	1
β-strand	344	1	6
α-helix	345	1
β-strand	352-357	6	4
α-helix	360-361	2
β-strand	369	1	5
α-helix	370-371	2
β-strand	374-380	7	4
α-helix	383-385	3
α-helix	386-402	17
α-helix	404-406	3
α-helix	407-410	4
α-helix	416-438	23

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	7
α-helix	11-27	17
β-strand	30	1	8
β-strand	36	1	8
β-strand	51-53	3	9
α-helix	55-57	3
β-strand	59-61	3	9
β-strand	65-67	3	7
α-helix	70-77	8
α-helix	87-89	3
β-strand	91-92	2	7
α-helix	108-110	3
α-helix	113-126	14
β-strand	133-138	6	7
α-helix	142-145	4
α-helix	147-158	12
β-strand	165-169	5	7
α-helix	181-192	12
β-strand	198-202	5	7
α-helix	204-213	10
α-helix	222-233	12
α-helix	238-241	4
α-helix	250-256	7
β-strand	265-267	3	7
β-strand	271	1	10
α-helix	286-293	8
α-helix	296-298	3
β-strand	310	1	11
β-strand	314-315	2	12
α-helix	324-336	13
α-helix	338-340	3
β-strand	341	1	11
β-strand	365	1	10
β-strand	367-368	2	12
β-strand	369	1	7
α-helix	374-388	15
α-helix	389-391	3
α-helix	396-399	4
α-helix	405-421	17

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

>5W3F_1 Tubulin alpha-1 chain (chains A)
MREVISINVGQAGCQIGNACWELYSLEHGIKPDGHLEDGLSKPKGGEEGFSTFFHETGYG
KFVPRAIYVDLEPNVIDEVRNGPYKDLFHPEQLISGKEDAANNYARGHYTVGREILGDVL
DRIRKLADQCDGLQGFLFTHSLGGGTGSGLGSLLLEELSAEYGKKSKLEFAVYPAPQVST
SVVEPYNTVLTTHTTLEHADCTFMVDNEAIYDMCKRNLDIPRPSFANLNNLIAQVVSSVT
ASLRFDGSLNVDLNEFQTNLVPYPRIHFPLVSYSPVLSKSKAFHESNSVSEITNACFEPG
NQMVKCDPRDGKYMATCLLYRGDVVTRDVQRAVEQVKNKKTVQLVDWCPTGFKIGICYEP
PTATPNSQLATVDRAVCMLSNTTSIAEAWKRIDRKFDLMYAKRAFVHWYVGEGMEEGEFT
EAREDLAALERDYIEVGADSYAEEEEF

Sequence of entity 2 (B), FASTA

>5W3F_2 Tubulin beta chain (chains B)
MREIIHISTGQCGNQIGAAFWETICGEHGLDFNGTYHGHDDIQKERLNVYFNEASSGKWV
PRSINVDLEPGTIDAVRNSAIGNLFRPDNYIFGQSSAGNVWAKGHYTEGAELVDSVMDVI
RREAEGCDSLQGFQITHSLGGGTGSGMGTLLISKIREEFPDRMMATFSVLPSPKTSDTVV
EPYNATLSVHQLVEHSDETFCIDNEALYDICQRTLKLNQPSYGDLNNLVSSVMSGVTTSL
RYPGQLNSDLRKLAVNLVPFPRLHFFMVGYAPLTAIGSQSFRSLTVPELTQQMFDAKNMM
AAADPRNGRYLTVAAFFRGKVSVKEVEDEMHKVQSKNSDYFVEWIPNNVQTAVCSVAPQG
LDMAATFIANSTSIQELFKRVGDQFSAMFKRKAFLHWYTSEGMDELEFSEAESNMNDLVS
EYQQYQEATVEDDEEVDENGDFGAPQNQDEPITENFE

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	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…
5W3H 4.0 Å, Yeast microtubule stabilized with epothilone
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…

Browse structure collections

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