6DPU: Undecorated GMPCPP microtubule

Undecorated GMPCPP microtubule. Determined by electron microscopy at 3.1 Å resolution. Released 4 Jul 2018.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Sus scrofa
Chains: 12
Atoms: 40,650
Mol. weight: 607.23 kDa
Ligands: G2P, MG, GTP
Released: 4 Jul 2018

Explore 6DPU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DPU contains 319 α-helices and 204 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, C, E, J, K and L: 27 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-107	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	1
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-205	6	1
α-helix	206-217	12
α-helix	224-243	20
β-strand	248	1	3
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	3
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	351-356	6	3
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-410	6
α-helix	415-436	22

Chain B: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	4
α-helix	10-27	18
β-strand	30	1	5
β-strand	35	1	6
β-strand	36	1	5
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	6
β-strand	60-63	4	6
β-strand	65-69	5	4
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	4
α-helix	103-107	5
α-helix	110-128	19
β-strand	132-140	9	4
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	4
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	4
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
β-strand	246-248	3	7
α-helix	252-259	8
β-strand	267-268	2	4
β-strand	269-273	5	7
α-helix	279-281	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	7
α-helix	307-309	3
β-strand	312-321	10	7
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	7
β-strand	351-356	6	7
α-helix	359-360	2
β-strand	373-381	9	7
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-436	22

Chains D, F, G, H and I: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-27	18
β-strand	30	1	12
β-strand	35	1	13
β-strand	36	1	12
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	13
β-strand	60-63	4	13
β-strand	65-69	5	11
α-helix	72-80	9
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	11
α-helix	103-107	5
α-helix	110-128	19
β-strand	132-140	9	11
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	11
α-helix	183-197	15
β-strand	200-205	6	11
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
β-strand	246-248	3	14
α-helix	252-259	8
β-strand	267-268	2	11
β-strand	269-273	5	14
α-helix	279-281	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	14
α-helix	307-309	3
β-strand	312-321	10	14
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	14
β-strand	351-356	6	14
α-helix	359-360	2
β-strand	373-381	9	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-436	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C, E, J, K, L	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D, F, G, H, I	protein	445	Sus scrofa	P02554 (AlphaFold model)

Sequence of entity 1 (A, C, E, J, K, L), FASTA

>6DPU_1 Tubulin alpha-1B chain (chains A, C, E, J, K, L)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D, F, G, H, I), FASTA

>6DPU_2 Tubulin beta chain (chains B, D, F, G, H, I)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Ligands and cofactors

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

Primary citation

Separating the effects of nucleotide and EB binding on microtubule structure. Zhang, R., LaFrance, B., Nogales, E. Proc Natl Acad Sci U S A (2018) 115:E6191-E6200. DOI 10.1073/pnas.1802637115 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

Browse more

6DPU is part of these collections:

Motor proteins and the cytoskeleton

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