5MJS: Tubulin beta chain

S. pombe microtubule copolymerized with GTP and Mal3-143. Determined by electron microscopy at 4.6 Å resolution. Released 20 Dec 2017.

Method: Electron microscopy
Resolution: 4.6 Å
Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Chains: 9
Atoms: 28,114
Mol. weight: 408.55 kDa
Ligands: GTP, GDP
Released: 20 Dec 2017

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

Secondary structure: helices and β-sheets

5MJS contains 161 α-helices and 148 β-strands across 9 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, B, C and J: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	11-27	17
β-strand	30	1	2
β-strand	36	1	2
β-strand	51-52	2	3
β-strand	60-61	2	3
β-strand	63-67	5	1
α-helix	73-78	6
β-strand	91-92	2	1
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-124	17
β-strand	130-138	9	1
α-helix	143-147	5
α-helix	148-156	9
β-strand	163-169	7	1
α-helix	170-172	3
α-helix	181-192	12
β-strand	198-202	5	1
α-helix	204-210	7
α-helix	211-215	5
α-helix	222-241	20
β-strand	244	1	4
α-helix	252-255	4
β-strand	263-265	3	1
β-strand	268-270	3	4
α-helix	285-290	6
β-strand	309	1	5
β-strand	312-318	7	4
α-helix	323-335	13
β-strand	340	1	5
β-strand	348-353	6	4
β-strand	362-368	7	4
β-strand	369	1	1
α-helix	374-385	12
α-helix	395-398	4
α-helix	404-425	22

Chain D: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	5-16	12
α-helix	23-27	5
α-helix	33-36	4
α-helix	45-47	3
α-helix	55-63	9
α-helix	65-72	8
α-helix	80-83	4
α-helix	92-98	7
α-helix	113-116	4

Chains E, F, G and H: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6-8	3	7
β-strand	9	1	8
α-helix	10-26	17
α-helix	52-54	3
β-strand	57-59	3	9
β-strand	65-67	3	9
β-strand	69	1	7
β-strand	71-72	2	8
α-helix	80-84	5
β-strand	96-97	2	8
α-helix	107-110	4
α-helix	115-118	4
α-helix	119-129	11
β-strand	136	1	6
β-strand	139-142	4	7
α-helix	149-165	17
β-strand	170-173	4	7
α-helix	189-192	4
β-strand	204-206	3	7
α-helix	210-219	10
α-helix	228-246	19
β-strand	252	1	10
α-helix	256-261	6
β-strand	275-277	3	10
α-helix	282-285	4
α-helix	292-299	8
α-helix	302-304	3
β-strand	305	1	10
α-helix	315	1
β-strand	316-325	10	10
α-helix	329-339	11
β-strand	355-360	6	10
α-helix	362-365	4
β-strand	377-385	9	10
α-helix	389-402	14
α-helix	410-413	4
α-helix	420-440	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta chain	A, B, C, J	protein	429	Schizosaccharomyces pombe (strain 972 / ATCC 24843)	P05219 (AlphaFold model)
Microtubule integrity protein mal3	D	protein	143	Schizosaccharomyces pombe (strain 972 / ATCC 24843)	Q10113 (AlphaFold model)
Tubulin alpha-1 chain	E, F, G, H	protein	444	Schizosaccharomyces pombe (strain 972 / ATCC 24843)	P04688 (AlphaFold model)

Sequence of entity 1 (A, B, C, J), FASTA

>5MJS_1 Tubulin beta chain (chains A, B, C, J)
MREIVHIQAGQCGNQVGAAFWSTIADEHGLDSAGIYHGTSEAQHERLNVYFNEAAGGKYV
PRAVLVDLEPGTMDAVKSGKFGNLFRPDNIIYGQSGAGNIWAKGHYTEGAELADAVLDVV
RREAEACDALQGFQLTHSLGGGTGSGMGTLLLSKIREEYPDRMMATFSVAPAPKSSDTVV
EPYNATLSMHQLVENSDETFCIDNEALSSIFANTLKIKSPSYDDLNHLVSAVMAGVTTSF
RFPGELNSDLRKLAVNMVPFPRLHFFMVGFAPLAAIGSSSFQAVSVPELTQQMFDANNMM
VAADPRHGRYLTVAALFRGKVSMKEVDEQIRSVQTKNSAYFVEWIPDNVLKAVCSVPPKD
LKMSATFIGNSTSIQEIFRRLGDQFSAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQEAG

Sequence of entity 2 (D), FASTA

>5MJS_2 Microtubule integrity protein mal3 (chains D)
MSESRQELLAWINQVTSLGLTRIEDCGKGYAMIQIFDSIYQDIPLKKVNFECNNEYQYIN
NWKVLQQVFLKKGIDKVVDPERLSRCKMQDNLEFVQWAKRFWDQYYPGGDYDALARRGNR
GPANTRVMNSSAGATGPSRRRQV

Sequence of entity 3 (E, F, G, H), FASTA

>5MJS_3 Tubulin alpha-1 chain (chains E, F, G, H)
MREVISVHVGQAGVQIGNACWELYCLEHGIGPDGFPTENSEVHKNNSYLNDGFGTFFSET
GQGKFVPRSIYVDLEPNVIDQVRTGPYKDLFHPEQMVTGKEDASNNYARGHYTVGKEMID
SVLERIRRMADNCSGLQGFLVFHSFGGGTGSGLGALLLERLNMEYGKKSNLQFSVYPAPQ
VSTSVVEPYNSVLTTHATLDNSDCTFMVDNEACYDICRRNLDIERPTYENLNRLIAQVVS
SITASLRFAGSLNVDLNEFQTNLVPYPRIHFPLVTYSPIVSAAKAFHESNSVQEITNQCF
EPYNQMVKCDPRTGRYMATCLLYRGDVIPRDVQAAVTSIKSRRTIQFVDWCPTGFKIGIC
YEPPQHVPGSGIAKVNRAVCMLSNTTSIAEAWSRLDHKFDLMYSKRAFVHWYVGEGMEEG
EFSEAREDLAALERDYEEVGQDSM

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	4

Primary citation

Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics. von Loeffelholz, O., Venables, N.A., Drummond, D.R. et al. Nat Commun (2017) 8:2110-2110. DOI 10.1038/s41467-017-02241-5 · PubMed

Other PDB entries of the same protein (UniProt P05219 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8M 4.5 Å, S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state

Browse structure collections

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