5ND4: Kinesin-like protein KIF20A

Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx. Determined by electron microscopy at 4.4 Å resolution. Released 4 Oct 2017.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Mus musculus, Bos taurus
Chains: 3
Atoms: 9,435
Mol. weight: 152.19 kDa
Ligands: TA1, GDP, GTP, ALF
Released: 4 Oct 2017

Explore 5ND4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ND4 contains 57 α-helices and 50 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	7
α-helix	11-26	16
β-strand	65-69	5	7
α-helix	72-75	4
α-helix	77-80	4
β-strand	92-94	3	7
α-helix	103-107	5
α-helix	109-128	20
β-strand	134	1	8
β-strand	135-139	5	7
α-helix	148-160	13
β-strand	165	1	8
β-strand	167-170	4	7
α-helix	183-195	13
β-strand	200-203	4	7
α-helix	207-215	9
α-helix	224-238	15
β-strand	248	1	7
α-helix	252-259	8
β-strand	269	1	7
β-strand	277	1	9
α-helix	288-291	4
α-helix	293-295	3
α-helix	298-300	3
β-strand	312-321	10	7
α-helix	325-336	12
β-strand	343	1	7
β-strand	351-355	5	7
β-strand	368	1	9
β-strand	373-381	9	7
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: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	10-26	17
β-strand	30	1	11
β-strand	36	1	11
α-helix	49-52	4
β-strand	65-69	5	10
α-helix	72-78	7
α-helix	83-86	4
α-helix	89-91	3
β-strand	92-94	3	10
α-helix	105-109	5
α-helix	111-126	16
β-strand	132-140	9	10
α-helix	144-148	5
α-helix	149-160	12
β-strand	165-172	8	10
α-helix	183-194	12
β-strand	200-205	6	10
α-helix	206-215	10
α-helix	224-242	19
β-strand	248	1	12
α-helix	252-259	8
β-strand	267-268	2	10
β-strand	270-271	2	12
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	12
α-helix	325-338	14
β-strand	351-356	6	12
β-strand	374-381	8	12
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-434	20

Chain C: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	1
α-helix	64	1
β-strand	65-70	6	2
α-helix	71-74	4
α-helix	75-80	6
β-strand	87-90	4	3
β-strand	94-100	7	3
β-strand	115-121	7	3
β-strand	124-126	3	2
α-helix	132-135	4
α-helix	136-140	5
α-helix	141-149	9
β-strand	153-159	7	2
α-helix	165-169	5
β-strand	171	1	4
β-strand	176	1	4
α-helix	178-189	12
β-strand	297-308	12	2
β-strand	311-314	4	2
α-helix	318-319	2
β-strand	329-331	3	5
β-strand	339-341	3	5
β-strand	346-347	2	2
α-helix	351-364	14
β-strand	367	1	6
β-strand	377	1	6
β-strand	380-390	11	2
β-strand	399-407	9	2
α-helix	408-411	4
α-helix	414-417	4
α-helix	421-448	28
α-helix	454-456	3
α-helix	457-459	3
α-helix	462-471	10
β-strand	476-483	8	2
α-helix	490-505	16
β-strand	507	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinesin-like protein KIF20A	C	protein	501	Mus musculus	P97329 (AlphaFold model)
Tubulin alpha chain	A	protein	412	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B	protein	426	Bos taurus	Q6B856 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>5ND4_1 Kinesin-like protein KIF20A (chains C)
SPILESTAADLRSVVRKDLLSDCSVISASLEDKQALLEDTSEKVKVYLRIRPFLTSELDR
QEDQGCVCIENTETLVLQAPKDSFALKSNERGVGQATHKFTFSQIFGPEVGQVAFFNLTM
KEMVKDVLKGQNWLIYTYGVTNSGKTYTIQGTSKDAGILPQSLALIFNSLQGQLHPTPDL
KPLLSNEVIWLDSKQIRQEEMKKLSLLIGGLQEEELSTSVKKRVHTESRIGASNSFDSGV
AGLSSTSQFTSSSQLDETSQLWAQPDTVPVSVPADIRFSVWISFFEIYNELLYDLLEPPS
HQHKRQTLRLCEDQNGNPYVKDLNWIHVRDVEEAWKLLKVGRKNQSFASTHMNQQSSRSH
SIFSIRILHLQGEGDIVPKISELSLCDLAGSERCKHQKSGERLKEAGNINTSLHTLGRCI
AALRQNQQNRSKQNLIPFRDSKLTRVFQGFFTGRGRSCMIVNVNPCASTYDETLHAAKFS
ALASQLVHAPPVHLGIPSLHS

Sequence of entity 2 (A), FASTA

>5ND4_2 Tubulin alpha chain (chains A)
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGHVPRAVFVDLEPTVIDEVRTGTYRQLF
HPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFSVFHSFGGGTGS
GFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNE
AIYDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDLTEFQTNLVPYPRGHF
PLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKD
VNAAIATIKTKRTIQFVDWCPTGFKVGINYEPPTVVPGGDLAKVQRAVCMLSNTTAIAEA
WARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS

Sequence of entity 3 (B), FASTA

>5ND4_3 Tubulin beta-2B chain (chains B)
REIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYVP
RAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVR
KESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVE
PYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLR
FPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMMA
ACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGL
KMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSE
YQQYQD

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
ALF	Tetrafluoroaluminate ion	Al F4	1
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry. Atherton, J., Yu, I.M., Cook, A. et al. Elife (2017) 6. DOI 10.7554/eLife.27793 · PubMed

Other PDB entries of the same protein (UniProt P97329 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LEF 2.09 Å, Rab6A:Kif20A complex
8BJS 2.73 Å, Apo KIF20A[55-510] crystal structure
8F1A 3.1 Å, Apo KIF20A[1-565] class-1 in complex with a microtubule
8F18 3.2 Å, Apo KIF20A[1-565] class-2 in complex with a microtubule
5ND2 5.8 Å, Microtubule-bound MKLP2 motor domain in the presence of ADP
5ND3 6.1 Å, Microtubule-bound MKLP2 motor domain in the with no nucleotide
5ND7 7.9 Å, Microtubule-bound MKLP2 motor domain in the presence of AMPPNP

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