7M18: HeLa-tubulin

HeLa-tubulin in complex with cryptophycin 1. Determined by electron microscopy at 3.38 Å resolution. Released 8 Sept 2021.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 16
Atoms: 54,064
Mol. weight: 818.46 kDa
Ligands: GTP, GDP, YNP
Released: 8 Sept 2021

Explore 7M18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M18 contains 336 α-helices and 296 β-strands across 16 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, C, E, G, I, K, M and O: 24 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	9
β-strand	9	1	10
α-helix	11-27	17
α-helix	48-51	4
β-strand	53-54	2	11
β-strand	62-63	2	11
β-strand	68	1	10
α-helix	75-79	5
α-helix	88	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-138	7	9
α-helix	145-149	5
α-helix	150-160	11
β-strand	167-169	3	9
β-strand	171-172	2	12
α-helix	175-177	3
α-helix	183-191	9
β-strand	200-201	2	9
β-strand	204-205	2	12
α-helix	206-215	10
α-helix	224-244	21
α-helix	252-259	8
α-helix	288-295	8
α-helix	307-309	3
β-strand	316	1	13
β-strand	319-320	2	14
α-helix	325-335	11
β-strand	352	1	13
β-strand	355-356	2	14
α-helix	359-363	5
α-helix	368-370	3
α-helix	382-384	3
α-helix	385-397	13
α-helix	405-409	5
α-helix	417-434	18

Chains B, D, F, H, J, L, N and P: 18 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	9	1	2
α-helix	11-28	18
β-strand	30	1	3
β-strand	36	1	3
α-helix	47-49	3
β-strand	51-53	3	4
β-strand	59-61	3	4
β-strand	63	1	1
β-strand	66	1	2
α-helix	73-76	4
α-helix	110-124	15
β-strand	129-136	8	1
α-helix	146-158	13
β-strand	166	1	1
β-strand	169-170	2	5
α-helix	181-195	15
β-strand	199-200	2	1
β-strand	202-203	2	5
α-helix	204-211	8
α-helix	222-235	14
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	1
β-strand	269-270	2	6
α-helix	286-293	8
β-strand	299	1	6
α-helix	305-307	3
β-strand	310	1	7
β-strand	313	1	8
β-strand	314-318	5	6
α-helix	326-336	11
β-strand	349	1	8
β-strand	352-354	3	6
α-helix	356-358	3
β-strand	364-368	5	6
β-strand	371	1	7
α-helix	372-374	3
α-helix	375-389	15
α-helix	395-401	7
α-helix	405-426	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-3 chain	B, D, F, H, J, L, N, P	protein	450	Homo sapiens	Q13509 (AlphaFold model)
Tubulin alpha-1B chain	A, C, E, G, I, K, M, O	protein	451	Homo sapiens	P68363 (AlphaFold model)

Sequence of entity 1 (B, D, F, H, J, L, N, P), FASTA

>7M18_1 Tubulin beta-3 chain (chains B, D, F, H, J, L, N, P)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPK

Sequence of entity 2 (A, C, E, G, I, K, M, O), FASTA

>7M18_2 Tubulin alpha-1B chain (chains A, C, E, G, I, K, M, O)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	8
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	8
YNP	Cryptophycin 1	C35 H43 Cl N2 O8	8

Primary citation

Conformational changes in tubulin upon binding cryptophycin-52 reveal its mechanism of action. Eren, E., Watts, N.R., Sackett, D.L. et al. J Biol Chem (2021) 297:101138-101138. DOI 10.1016/j.jbc.2021.101138 · PubMed

Other PDB entries of the same protein (UniProt Q13509 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
9WD9 2.26 Å, GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
9WD7 2.34 Å, GMPCPP-stabilizsd human alpha1A/beta3 microtubule
9WDA 2.35 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule
9WDB 2.39 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
22AK 2.41 Å, GDP human alpha1A/beta3 microtubule
22AJ 2.48 Å, GDP human alpha1A/beta3 S239C microtubule
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
6WSL 3.1 Å, Cryo-EM structure of VASH1-SVBP bound to microtubules
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52

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