2WBE: Kinesin-5-Tubulin Complex with AMPPNP

Kinesin-5-Tubulin Complex with AMPPNP. Determined by electron microscopy at 9.4 Å resolution. Released 24 Mar 2009.

Method: Electron microscopy
Resolution: 9.4 Å
Organisms: BOS TAURUS, DROSOPHILA MELANOGASTER
Chains: 3
Atoms: 9,385
Mol. weight: 144.3 kDa
Ligands: MG, GTP, GDP, TA1
Released: 24 Mar 2009

Explore 2WBE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WBE contains 57 α-helices and 53 β-strands across 3 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.

Chain A: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-26	17
β-strand	65-69	5	1
α-helix	72-80	9
β-strand	92-94	3	1
α-helix	103-107	5
α-helix	109-128	20
β-strand	134-139	6	1
α-helix	144-149	6
α-helix	150-160	11
β-strand	165	1	1
β-strand	167-170	4	1
α-helix	184-194	11
β-strand	200-203	4	1
α-helix	206-215	10
α-helix	224-242	19
α-helix	252-259	8
β-strand	269-271	3	1
β-strand	277	1	2
α-helix	288-291	4
α-helix	293-296	4
β-strand	312-321	10	1
α-helix	325-336	12
β-strand	343	1	1
β-strand	351-355	5	1
β-strand	368	1	2
β-strand	373-381	9	1
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-429	15
α-helix	431-434	4

Chain B: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
β-strand	6-9	4	3
α-helix	12-26	15
β-strand	30	1	4
β-strand	36	1	4
α-helix	49-52	4
β-strand	55	1	5
β-strand	61	1	5
β-strand	65-69	5	3
α-helix	72-78	7
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	3
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-139	6	3
α-helix	144-148	5
α-helix	149-160	12
β-strand	165-170	6	3
α-helix	184-194	11
β-strand	200-202	3	3
α-helix	206-214	9
α-helix	224-242	19
β-strand	248	1	6
α-helix	252-259	8
β-strand	267-268	2	3
β-strand	269-271	3	6
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	6
α-helix	325-338	14
β-strand	351-356	6	6
β-strand	375-381	7	6
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-436	22

Chain C: 17 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	7
α-helix	8	1
β-strand	9-14	6	8
α-helix	15-18	4
α-helix	19-24	6
β-strand	28	1	9
β-strand	30-33	4	10
β-strand	37-40	4	10
β-strand	50-53	4	10
β-strand	56-58	3	8
α-helix	64-67	4
α-helix	68-72	5
α-helix	73-81	9
β-strand	85-90	6	8
α-helix	97-101	5
β-strand	103	1	11
β-strand	119	1	11
α-helix	121-135	15
β-strand	140-150	11	8
β-strand	153-156	4	8
β-strand	168-170	3	12
β-strand	178-180	3	12
β-strand	186-188	3	8
α-helix	191-205	15
α-helix	212-218	7
β-strand	220-229	10	8
β-strand	239-241	3	13
β-strand	242-249	8	8
α-helix	250-252	3
α-helix	275-289	15
α-helix	296-298	3
α-helix	300-304	5
α-helix	306-310	5
β-strand	314-321	8	8
β-strand	324	1	9
α-helix	325-327	3
α-helix	328-342	15
β-strand	345-346	2	7
β-strand	352-353	2	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1D chain	A	protein	451	BOS TAURUS	Q2HJ86 (AlphaFold model)
Tubulin beta-2B chain	B	protein	445	BOS TAURUS	Q6B856 (AlphaFold model)
Bipolar kinesin krp-130	C	protein	373	DROSOPHILA MELANOGASTER	P46863 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2WBE_1 TUBULIN ALPHA-1D CHAIN (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>2WBE_2 TUBULIN BETA-2B CHAIN (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C), FASTA

>2WBE_3 BIPOLAR KINESIN KRP-130 (chains C)
GHMASMDISGGNTSRQPQKKSNQNIQVYVRVRPLNSRERCIRSAEVVDVVGPREVVTRHT
LDSKLTKKFTFDRSFGPESKQCDVYSVVVSPLIEEVLNGYNCTVFAYGQTGTGKTHTMVG
NETAELKSSWEDDSDIGIIPRALSHLFDELRMMEVEYTMRISYLELYNEELCDLLSTDDT
TKIRIFDDSTKKGSVIIQGLEEIPVHSKDDVYKLLEKGKERRKTATTLMNAQSSRSHTVF
SIVVHIRENGIEGEDMLKIGKLNLVDLAGSENVSKAGNEKGIRVRETVNINQSLLTLGRV
ITALVDRAPHVPYRESKLTRLLQESLGGRTKTSIIATISPGHKDIEETLSTLEYAHRAKN
IQNKPEVNQKLTK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
TA1	Taxol	C47 H51 N O14	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

9-Angstrom Structure of a Microtubule-Bound Mitotic Motor. Bodey, A.J., Kikkawa, M., Moores, C.A. J Mol Biol (2009) 388:218. DOI 10.1016/J.JMB.2009.03.008 · PubMed

Other PDB entries of the same protein (UniProt Q2HJ86 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TVK 2.89 Å, The binding mode of epothilone A on a,b-tubulin by electron crystallography
7RRO 3.4 Å, Structure of the 48-nm repeat doublet microtubule from bovine tracheal cilia
9CPB 3.52 Å, Atomic model of bovine Fallopian tube cilia doublet microtubule (48-nm periodicity)
1SA0 3.58 Å, Tubulin-colchicine: stathmin-like domain complex
1Z2B 4.1 Å, Tubulin-colchicine-vinblastine: stathmin-like domain complex
1SA1 4.2 Å, Tubulin-podophyllotoxin: stathmin-like domain complex
2XRP 8.2 Å, Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF and 3HKE) Docked into…
4ATX 8.2 Å, Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin dimer,…
4ATU 8.3 Å, Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM…
3IZ0 8.6 Å, Human Ndc80 Bonsai Decorated Microtubule
4CK6 9.2 Å, Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in the ADP.AlFx…
4CK7 9.2 Å, Pseudo-atomic model of microtubule-bound human kinesin-5 motor domain in presence of…

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