3DCO: Kinesin-like protein Nod

Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule. Determined by electron microscopy at 11.0 Å resolution. Released 10 Feb 2009.

Method: Electron microscopy
Resolution: 11.0 Å
Organisms: Drosophila melanogaster, Bos taurus
Chains: 3
Atoms: 8,977
Mol. weight: 140.68 kDa
Ligands: MG, ADP, ZN, GTP
Released: 10 Feb 2009

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

Secondary structure: helices and β-sheets

3DCO contains 54 α-helices and 44 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	3
α-helix	10-26	17
β-strand	65-69	5	3
α-helix	72-80	9
β-strand	92-94	3	3
α-helix	103-107	5
α-helix	109-128	20
β-strand	134-139	6	3
α-helix	144-149	6
α-helix	150-160	11
β-strand	165	1	3
β-strand	167-170	4	3
α-helix	184-194	11
β-strand	200-203	4	3
α-helix	206-215	10
α-helix	224-242	19
α-helix	252-259	8
β-strand	269-271	3	3
β-strand	277	1	4
α-helix	288-291	4
α-helix	293-296	4
β-strand	312-321	10	3
α-helix	325-336	12
β-strand	343	1	3
β-strand	351-355	5	3
β-strand	368	1	4
β-strand	373-381	9	3
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	5
β-strand	6-9	4	5
α-helix	12-26	15
β-strand	30	1	6
β-strand	36	1	6
α-helix	49-52	4
β-strand	55	1	7
β-strand	61	1	7
β-strand	65-69	5	5
α-helix	72-78	7
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-139	6	5
α-helix	144-148	5
α-helix	149-160	12
β-strand	165-170	6	5
α-helix	184-194	11
β-strand	200-202	3	5
α-helix	206-214	9
α-helix	224-242	19
β-strand	248	1	8
α-helix	252-259	8
β-strand	267-268	2	5
β-strand	269-271	3	8
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	8
α-helix	325-338	14
β-strand	351-356	6	8
β-strand	375-381	7	8
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 N: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	1
α-helix	16-18	3
β-strand	30-31	2	2
β-strand	40-43	4	2
β-strand	46-49	4	2
β-strand	52-54	3	1
α-helix	60-67	8
α-helix	69-77	9
β-strand	81-86	6	1
α-helix	93-97	5
α-helix	102-104	3
α-helix	107-109	3
α-helix	112-126	15
β-strand	136-145	10	1
β-strand	149-151	3	1
β-strand	160	1	1
β-strand	172-173	2	1
α-helix	177-189	13
β-strand	205-214	10	1
β-strand	219-226	8	1
α-helix	227-229	3
α-helix	252-264	13
α-helix	272-274	3
α-helix	276-280	5
β-strand	290-297	8	1
α-helix	301-303	3
α-helix	304-320	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein Nod	N	protein	344	Drosophila melanogaster	P18105 (AlphaFold model)
Bovine Alpha Tubulin	A	protein	451	Bos taurus	P81947 (AlphaFold model)
Bovine Beta Tubulin	B	protein	445	Bos taurus	Q6B856 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>3DCO_1 Kinesin-like protein Nod (chains N)
MASDYKDDDDKRRRGMEGAKLSAVRIAVREAPYRQFLGRREPSVVQFPPWSDGKSLIVDQ
NEFHFDHAFPATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSMGMTPPGEI
LPEHLGILPRALGDIFERVTARQENNKDAIQVYASFIEIYNEKPFDLLGSTPHMPMVAAR
CQRCTCLPLHSQADLHHILELGTRNRRVRPTNMNSNSSRSHAIVTIHVKSKTHHSRMNIV
DLAGSEGVRRTGHEGVARQEGVNINLGLLSINKVVMSMAAGHTVIPYRDSVLTTVLQASL
TAQSYLTFLACISPHQCDLSETLSTLRFGTSAKAAALEHHHHHH

Sequence of entity 2 (A), FASTA

>3DCO_2 Bovine Alpha Tubulin (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>3DCO_3 Bovine Beta Tubulin (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ZN	Zinc ion	Zn	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

ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement. Cochran, J.C., Sindelar, C.V., Mulko, N.K. et al. Cell (2009) 136:110-122. DOI 10.1016/j.cell.2008.11.048 · PubMed

Other PDB entries of the same protein (UniProt P18105 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3DC4 1.9 Å, Crystal structure of the Drosophila kinesin family member NOD in complex with ADP
3DCB 2.5 Å, Crystal structure of the Drosophila kinesin family member NOD in complex with AMPPNP
3PXN 2.6 Å, Crystal structure of the Drosophila kinesin family member Kin10/NOD in complex with…

Browse structure collections

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