3IZ0: Human Ndc80 Bonsai Decorated Microtubule

Human Ndc80 Bonsai Decorated Microtubule. Determined by electron microscopy at 8.6 Å resolution. Released 13 Oct 2010.

Method: Electron microscopy
Resolution: 8.6 Å
Organisms: Bos taurus, Homo sapiens
Chains: 6
Atoms: 12,154
Mol. weight: 232.61 kDa
Ligands: ZN, MG, GTP, GDP
Released: 13 Oct 2010

Explore 3IZ0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3IZ0 contains 76 α-helices and 35 β-strands across 6 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

Chains C and E: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	89-105	17
α-helix	122-134	13
α-helix	147-157	11
α-helix	166-170	5
α-helix	178-198	21
β-strand	214	1	7
β-strand	220	1	7
α-helix	222-236	15
α-helix	244-257	14

Chains D and F: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	11-21	11
α-helix	26-30	5
α-helix	33-35	3
α-helix	42-57	16
α-helix	61-65	5
α-helix	66-68	3
α-helix	76-79	4
α-helix	83-98	16
α-helix	106-110	5
α-helix	114-148	35
α-helix	150-153	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
alpha tubulin, Chain A from PDB 1JFF	A	protein	451	Bos taurus	Q2HJ86 (AlphaFold model)
beta tubulin, Chain B from PDB 1JFF	B	protein	445	Bos taurus	Q6B856 (AlphaFold model)
NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai)	C, E	protein	315	Homo sapiens	O14777 (AlphaFold model), Q9HBM1 (AlphaFold model)
NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai)	D, F	protein	250	Homo sapiens	Q8NBT2, Q9BZD4

Sequence of entity 1 (A), FASTA

>3IZ0_1 alpha tubulin, Chain A from PDB 1JFF (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>3IZ0_2 beta tubulin, Chain B from PDB 1JFF (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C, E), FASTA

>3IZ0_3 NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai) (chains C, E)
MIKDPRPLNDKAFIQQCIRQLCEFLTENGYAHNVSMKSLQAPSVKDFLKIFTFLYGFLCP
SYELPDTKFEEEVPRIFKDLGYPFALSKSSMYTVGAPHTWPHIVAALVWLIDCIKIHTAM
KESSPLFDDGQPWGEETEDGIMHNKLFLDYTIKCYESFMSGADSFDEMNAELQSKLKDLF
NVDAFKLESLEAKNRALNEQIARLEQERSTANKANAERLKRLQKSADLYKDRLGLEIRKI
YGEKLQFIFTNIDPKNPESPFMFSLHLNEARDYEVSDSAPHLEGLAEFQENVRKTNNFSA
FLANVRKAFTATVYQ

Sequence of entity 4 (D, F), FASTA

>3IZ0_4 NUF2-SPC24 chimera protein, Chain D from PDB 2VE7  (Ndc80 bonsai) (chains D, F)
GPLGSMETLSFPRYNVAEIVIHIRNKILTGADGKNLTKNDLYPNPKPEVLHMIYMRALQI
VYGIRLEHFYMMPVNSGVMYPHLMEGFLPFSNLVTHLDSFLPICRVNDFETADILCPKAK
RTSRFLSGIINFIHFREACRETYMEFLWQYKSSADKMQQLNAAHQEALMKLERLEKEVDE
DTTVTIPSAVYVAQLYHQVSKIEWEYECEPGMVKGIHHGPSVAQPIHLDSTQLSRKFISD
YLWSLVDTEW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
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

Primary citation

The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Alushin, G.M., Ramey, V.H., Pasqualato, S. et al. Nature (2010) 467:805-810. DOI 10.1038/nature09423 · 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…
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…
5M5I 9.3 Å, Pseudo-atomic model of microtubule-bound S.pombe kinesin-5 motor domain in the AMPPNP…

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