7LXB: HeLa-tubulin

HeLa-tubulin in complex with cryptophycin 52. Determined by electron microscopy at 3.26 Å resolution. Released 8 Sept 2021.

Method: Electron microscopy
Resolution: 3.26 Å
Organism: Homo sapiens
Chains: 16
Atoms: 54,280
Mol. weight: 818.57 kDa
Ligands: GDP, YGY, GTP
Released: 8 Sept 2021

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

Secondary structure: helices and β-sheets

7LXB contains 352 α-helices and 328 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: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	10-27	18
β-strand	54	1	2
β-strand	62	1	2
β-strand	65-68	4	1
α-helix	75-79	5
α-helix	84-86	3
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	134-138	5	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	1
α-helix	175-177	3
α-helix	183-191	9
α-helix	195-197	3
β-strand	200-204	5	1
α-helix	206-216	11
α-helix	226-243	18
α-helix	252-259	8
β-strand	262	1	3
β-strand	265	1	3
β-strand	269-270	2	4
β-strand	271	1	5
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	5
α-helix	307-309	3
β-strand	312	1	6
β-strand	315-316	2	4
β-strand	317-320	4	7
α-helix	325-335	11
β-strand	343	1	6
β-strand	353-356	4	7
α-helix	359-361	3
β-strand	374-375	2	7
β-strand	378-379	2	4
α-helix	385-400	16
α-helix	406-409	4
α-helix	416-434	19

Chains B, D, F, H, J, L, N and P: 21 helices, 22 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	41-43	3
α-helix	47-49	3
β-strand	52	1	10
β-strand	60	1	10
β-strand	63-66	4	8
α-helix	72-76	5
α-helix	82-84	3
α-helix	103-107	5
α-helix	113-125	13
β-strand	130-136	7	8
α-helix	142-146	5
α-helix	147-158	12
β-strand	165-170	6	8
β-strand	172	1	11
β-strand	175	1	11
α-helix	181-195	15
β-strand	198-203	6	8
α-helix	205-213	9
α-helix	224-241	18
α-helix	250-257	8
β-strand	265-266	2	8
β-strand	267-269	3	12
α-helix	286-293	8
α-helix	305-307	3
β-strand	310-312	3	13
β-strand	313	1	14
β-strand	315	1	12
β-strand	317	1	15
α-helix	323-335	13
α-helix	338-340	3
β-strand	341	1	13
β-strand	349	1	14
β-strand	353	1	15
α-helix	357-358	2
β-strand	367-369	3	12
β-strand	370-371	2	13
α-helix	374-390	17
α-helix	395-401	7
α-helix	405-426	22

Molecules and chains

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

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>7LXB_1 Tubulin alpha-1B chain (chains A, C, E, G, I, K, M, O)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>7LXB_2 Tubulin beta-3 chain (chains B, D, F, H, J, L, N, P)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPK

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	8
YGY	Cryptophycin 52	C36 H45 Cl N2 O8	8
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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 P68363 (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
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
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
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9HQ4 3.28 Å, TTLL11 bound to microtubule
7M18 3.38 Å, HeLa-tubulin in complex with cryptophycin 1

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