5JCO: Tubulin beta-3 chain

Structure and dynamics of single-isoform recombinant neuronal human tubulin. Determined by electron microscopy at 4.0 Å resolution. Released 4 May 2016.

Method: Electron microscopy
Resolution: 4.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 40,512
Mol. weight: 585.31 kDa
Ligands: GTP, MG, G2P
Released: 4 May 2016

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

Secondary structure: helices and β-sheets

5JCO contains 318 α-helices and 186 β-strands across 12 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, E and H: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	22
α-helix	10-28	19
β-strand	35	1	23
α-helix	48-51	4
β-strand	53-56	4	23
β-strand	60-63	4	23
β-strand	65-68	4	22
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-93	2	22
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-140	7	22
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	22
α-helix	173-174	2
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-205	6	22
α-helix	206-216	11
α-helix	224-243	20
β-strand	246	1	22
α-helix	252-259	8
β-strand	269-273	5	22
α-helix	280-283	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	22
α-helix	325-337	13
β-strand	343	1	22
β-strand	351-356	6	22
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	22
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Chains C, D, I, J, K and L: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
α-helix	10-27	18
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-52	2	15
α-helix	55-57	3
β-strand	60-61	2	15
β-strand	63-67	5	14
α-helix	70-78	9
α-helix	82-84	3
α-helix	87-89	3
β-strand	90-92	3	14
α-helix	101-105	5
α-helix	109-126	18
β-strand	130-138	9	14
α-helix	142	1
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	14
α-helix	181-195	15
β-strand	198-203	6	14
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
β-strand	244-246	3	16
α-helix	250-257	8
β-strand	265-266	2	14
β-strand	267-271	5	16
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	16
α-helix	305-307	3
β-strand	310-318	9	16
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	16
β-strand	349-354	6	16
α-helix	357-358	2
β-strand	364-371	8	16
α-helix	374-390	17
α-helix	395-399	5
α-helix	405-425	21

Chains F and G: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	20
α-helix	10-27	18
β-strand	35	1	21
α-helix	48-51	4
β-strand	53-56	4	21
β-strand	60-63	4	21
β-strand	65-68	4	20
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-93	2	20
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-140	7	20
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	20
α-helix	173-174	2
α-helix	175-177	3
α-helix	183-197	15
β-strand	200-205	6	20
α-helix	206-216	11
α-helix	224-243	20
β-strand	246	1	20
α-helix	252-259	8
β-strand	269-273	5	20
α-helix	280-283	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	20
α-helix	325-337	13
β-strand	343	1	20
β-strand	351-356	6	20
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	20
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-435	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-3 chain	C, D, I, J, K, L	protein	426	Homo sapiens	Q13509 (AlphaFold model)
Tubulin alpha-1A chain	A, B, E, F, G, H	protein	437	Homo sapiens	Q71U36 (AlphaFold model)

Sequence of entity 1 (C, D, I, J, K, L), FASTA

>5JCO_1 Tubulin beta-3 chain (chains C, D, I, J, K, L)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQ

Sequence of entity 2 (A, B, E, F, G, H), FASTA

>5JCO_2 Tubulin alpha-1A chain (chains A, B, E, F, G, H)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGV

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	6
MG	Magnesium ion	Mg	12
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	6

Primary citation

Structure and Dynamics of Single-isoform Recombinant Neuronal Human Tubulin. Vemu, A., Atherton, J., Spector, J.O. et al. J Biol Chem (2016) 291:12907-12915. DOI 10.1074/jbc.C116.731133 · 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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