7RS5: Kip3

Cryo-EM structure of Kip3 (AMPPNP) bound to Taxol-Stabilized Microtubules. Determined by electron microscopy at 3.9 Å resolution. Released 17 Aug 2022.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Sus scrofa, Saccharomyces cerevisiae
Chains: 27
Atoms: 86,121
Mol. weight: 1280.61 kDa
Ligands: ANP, TA1, GDP, MG
Released: 17 Aug 2022

Explore 7RS5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RS5 contains 486 α-helices and 477 β-strands across 27 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, c, d, e, f, g and h: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	27
α-helix	22-25	4
β-strand	34-38	5	28
β-strand	41-44	4	28
β-strand	64	1	29
β-strand	66	1	29
β-strand	68-71	4	28
β-strand	74-75	2	27
α-helix	82-97	16
β-strand	103-105	3	27
α-helix	128-143	16
β-strand	147-154	8	27
β-strand	157-159	3	27
β-strand	162-164	3	27
α-helix	173-175	3
β-strand	178-180	3	30
β-strand	186-188	3	30
β-strand	194	1	27
α-helix	199-212	14
β-strand	228-239	12	27
β-strand	251-257	7	27
α-helix	272-299	28
α-helix	311-315	5
β-strand	325-332	8	27
α-helix	336-338	3
α-helix	339-353	15

Chains A, C, E, G, I, L, N, P and R: 21 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	12-28	17
β-strand	35	1	2
β-strand	53-54	2	3
β-strand	60	1	2
β-strand	62-63	2	3
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	115-128	14
β-strand	132-140	9	1
α-helix	144-160	17
β-strand	165-171	7	1
α-helix	183-197	15
β-strand	200-204	5	1
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-244	5
β-strand	248	1	4
α-helix	252-259	8
β-strand	268-272	5	4
α-helix	280-283	4
α-helix	288-294	7
α-helix	307-309	3
β-strand	311-321	11	4
α-helix	325-338	14
β-strand	342-343	2	4
β-strand	351-355	5	4
α-helix	359-361	3
β-strand	373-381	9	4
α-helix	383-385	3
α-helix	386-400	15
α-helix	406-409	4
α-helix	415-437	23

Chains B, D, F, H, J, M, O, Q and S: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	10-27	18
β-strand	30	1	10
β-strand	36	1	10
α-helix	42-44	3
α-helix	49-51	3
β-strand	53-56	4	11
β-strand	60-63	4	11
β-strand	65-68	4	9
α-helix	74-80	7
α-helix	89-91	3
β-strand	92-93	2	9
α-helix	97-98	2
α-helix	103	1
α-helix	104-108	5
α-helix	112-114	3
α-helix	115-126	12
β-strand	132-140	9	9
α-helix	145-160	16
β-strand	165-172	8	9
β-strand	174	1	12
β-strand	177	1	12
α-helix	183-197	15
β-strand	200-205	6	9
α-helix	206-215	10
α-helix	224-240	17
β-strand	246-248	3	13
α-helix	252-259	8
β-strand	267-268	2	9
β-strand	269-272	4	13
α-helix	281-283	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	13
α-helix	307-309	3
β-strand	312-320	9	13
α-helix	325-338	14
β-strand	343	1	13
β-strand	351-356	6	13
α-helix	359-360	2
β-strand	374-381	8	13
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-434	20

Chain K: 9 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	14
α-helix	22-25	4
β-strand	90-94	5	15
β-strand	97-100	4	15
β-strand	147	1	16
β-strand	149	1	16
β-strand	151-154	4	15
β-strand	157-158	2	14
α-helix	165-180	16
β-strand	186-188	3	14
α-helix	211-226	16
β-strand	230-237	8	14
β-strand	240-242	3	14
β-strand	245-247	3	14
α-helix	256-258	3
β-strand	261-263	3	17
β-strand	269-271	3	17
β-strand	277	1	14
α-helix	282-295	14
β-strand	311-322	12	14
β-strand	334-340	7	14
α-helix	355-382	28
α-helix	394-398	5
β-strand	408-415	8	14
α-helix	419-421	3
α-helix	422-436	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1A chain	A, C, E, G, I, L, N, P, R	protein	451	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	B, D, F, H, J, M, O, Q, S	protein	445	Sus scrofa	P02554 (AlphaFold model)
yeast kinesin-8/ Kip3	K, a, b, c, d, e, f, g, h	protein	355	Saccharomyces cerevisiae

Sequence of entity 1 (A, C, E, G, I, L, N, P, R), FASTA

>7RS5_1 Tubulin alpha-1A chain (chains A, C, E, G, I, L, N, P, R)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D, F, H, J, M, O, Q, S), FASTA

>7RS5_2 Tubulin beta chain (chains B, D, F, H, J, M, O, Q, S)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (K, a, b, c, d, e, f, g, h), FASTA

>7RS5_3 yeast kinesin-8/ Kip3 (chains K, a, b, c, d, e, f, g, h)
MNVPETRQSSIVVAIRVRPFTSMEKTRLVIRKIVDCVDDRMLIFDPADRNSNATNKFSSQ
RRRHGGEIKFVFDKLFDETSSQARVYKETTSPLLDSVLDGFNSTVFAYGATGCGKTYTVS
GTPSQPGIIFLAMEELFNKITDLKDEKDFEISLSYLEIYNERIRDLLKPETPSKRLVIRE
DTQNHIKVANLSYHHPNTVEDVMDLVVQGNINRTTSPTEANEVSSRSHAVLQIHIMQTNK
LVDLTSQHTFATLSIIDLAGSERAAATRNRGIRLHEGANINRSLLALGNCINALCLNDGS
RSCHIPYRDSKLTRLLKFSLGGNCKTVMIVCISPSSSHYDETLNTLKYANRAKEI

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	9
TA1	Taxol	C47 H51 N O14	9
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	9
MG	Magnesium ion	Mg	18
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	9

Primary citation

Multimodal tubulin binding by the yeast kinesin-8, Kip3, underlies its motility and depolymerization. Arellano-Santoyo, H., Hernandez-Lopez, R.A., Stokasimov, E. et al. bioRxiv (2021). DOI 10.1101/2021.10.12.464151

Other PDB entries of the same protein (UniProt P02550 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7X4N 2.88 Å, Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin
9T1D 2.9 Å, Cryo-EM reconstruction of undecorated GDP microtubule
6MZG 3.21 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
7U0F 3.53 Å, HIV-1 Rev in complex with tubulin
8QAU 3.54 Å, Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
8X9P 3.54 Å, HURP (428-534)-alpha-tubulin-beta-tubulin complex
6MZE 3.6 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
6KIQ 3.62 Å, Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT
1TUB 3.7 Å, Tubulin alpha-beta dimer, electron diffraction
9EDT 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
9EEB 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
9EDR 3.8 Å, Tubulin Cofactors D,E,G,C and Tubulin complex -- TBCC N Terminus Bound to Tubulin

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