5ND3: Kinesin-like protein KIF20A

Microtubule-bound MKLP2 motor domain in the with no nucleotide. Determined by electron microscopy at 6.1 Å resolution. Released 4 Oct 2017.

Method: Electron microscopy
Resolution: 6.1 Å
Organisms: Mus musculus, Bos taurus
Chains: 3
Atoms: 9,076
Mol. weight: 157.88 kDa
Ligands: TA1, GDP, MG, GTP
Released: 4 Oct 2017

Explore 5ND3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ND3 contains 58 α-helices and 51 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: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	11-27	17
β-strand	65-69	5	5
α-helix	72-78	7
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	105-109	5
α-helix	111-128	18
β-strand	134-140	7	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	173-174	2
α-helix	183-193	11
α-helix	194-196	3
β-strand	200-201	2	5
β-strand	203	1	6
β-strand	204-205	2	5
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	6
α-helix	252-259	8
β-strand	266	1	5
β-strand	269-271	3	6
β-strand	277	1	7
α-helix	288-293	6
α-helix	294-296	3
β-strand	297	1	8
β-strand	300	1	8
β-strand	312	1	9
β-strand	314-321	8	6
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	9
α-helix	344	1
β-strand	351-355	5	6
β-strand	368	1	7
β-strand	373-380	8	6
α-helix	384-400	17
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-435	21

Chain B: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	10
α-helix	10-28	19
β-strand	30	1	11
β-strand	36	1	11
α-helix	44-51	6
β-strand	53-54	2	12
β-strand	62-63	2	12
β-strand	65-69	5	10
α-helix	72-78	7
β-strand	92-94	3	10
α-helix	105-109	5
α-helix	110-126	17
β-strand	132-140	9	10
α-helix	144-149	6
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-205	6	10
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-235	12
α-helix	241-243	3
α-helix	252-256	5
β-strand	268	1	10
β-strand	269-272	4	13
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	13
α-helix	325-338	14
α-helix	340-342	3
β-strand	351-356	6	13
β-strand	375-381	7	13
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-411	6
α-helix	415-436	22

Chain C: 14 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	62-64	3
β-strand	65-70	6	1
α-helix	71-72	2
α-helix	75-80	6
β-strand	87-90	4	2
β-strand	94-99	6	2
β-strand	116-121	6	2
β-strand	124-126	3	1
α-helix	132-135	4
α-helix	136-140	5
α-helix	141-148	8
β-strand	152-158	7	1
α-helix	165-169	5
β-strand	171	1	3
β-strand	176	1	3
α-helix	178-188	11
β-strand	297-308	12	1
β-strand	311-314	4	1
β-strand	330-332	3	4
β-strand	338-340	3	4
β-strand	347	1	1
α-helix	351-363	13
β-strand	380-390	11	1
β-strand	400-408	9	1
α-helix	409-411	3
α-helix	425-448	24
α-helix	457-460	4
α-helix	462-472	11
β-strand	475-483	9	1
α-helix	490-500	11

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	451	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B	protein	445	Bos taurus	Q6B856 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>5ND3_1 Kinesin-like protein KIF20A (chains C)
SPILESTAADLRSVVRKDLLSDCSVISASLEDKQALLEDTSEKVKVYLRIRPFLTSELDR
QEDQGCVCIENTETLVLQAPKDSFALKSNERGVGQATHKFTFSQIFGPEVGQVAFFNLTM
KEMVKDVLKGQNWLIYTYGVTNSGKTYTIQGTSKDAGILPQSLALIFNSLQGQLHPTPDL
KPLLSNEVIWLDSKQIRQEEMKKLSLLIGGLQEEELSTSVKKRVHTESRIGASNSFDSGV
AGLSSTSQFTSSSQLDETSQLWAQPDTVPVSVPADIRFSVWISFFEIYNELLYDLLEPPS
HQHKRQTLRLCEDQNGNPYVKDLNWIHVRDVEEAWKLLKVGRKNQSFASTHMNQQSSRSH
SIFSIRILHLQGEGDIVPKISELSLCDLAGSERCKHQKSGERLKEAGNINTSLHTLGRCI
AALRQNQQNRSKQNLIPFRDSKLTRVFQGFFTGRGRSCMIVNVNPCASTYDETLHAAKFS
ALASQLVHAPPVHLGIPSLHS

Sequence of entity 2 (A), FASTA

>5ND3_2 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>5ND3_3 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	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
5ND4 4.4 Å, Microtubule-bound MKLP2 motor domain in the presence of ADP.AlFx
5ND2 5.8 Å, Microtubule-bound MKLP2 motor domain in the presence of ADP
5ND7 7.9 Å, Microtubule-bound MKLP2 motor domain in the presence of AMPPNP

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