8F18: Apo KIF20A[1-565] class-2

Apo KIF20A[1-565] class-2 in complex with a microtubule. Determined by electron microscopy at 3.2 Å resolution. Released 20 Sept 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Sus scrofa, Mus musculus
Chains: 3
Atoms: 9,889
Mol. weight: 166.14 kDa
Ligands: TA1, GDP, GTP, MG
Released: 20 Sept 2023

Explore 8F18 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F18 contains 66 α-helices and 58 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: 26 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
β-strand	5-9	5	2
α-helix	10-27	18
α-helix	37-42	6
β-strand	53-55	3	3
β-strand	61-63	3	3
β-strand	65-68	4	2
α-helix	72-80	9
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-126	12
β-strand	132	1	1
β-strand	135-140	6	2
α-helix	148-160	13
β-strand	166-172	7	2
α-helix	173-174	2
α-helix	183-188	6
α-helix	191-196	6
β-strand	200-205	6	2
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-238	15
α-helix	240-242	3
β-strand	248	1	4
α-helix	252-257	6
β-strand	269-272	4	4
α-helix	279-281	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-337	13
β-strand	343	1	4
β-strand	351-356	6	4
α-helix	359-361	3
α-helix	368-370	3
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	406-409	4
α-helix	416-433	18
α-helix	438-439	2

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-65	3	5
α-helix	70-77	8
α-helix	87-89	3
β-strand	90	1	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	5
α-helix	143-158	16
β-strand	163-169	7	5
α-helix	170-172	3
α-helix	181-193	13
β-strand	198-202	5	5
α-helix	204-213	10
α-helix	222-236	15
α-helix	238-241	4
β-strand	246	1	8
α-helix	250-255	6
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	276-281	6
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
β-strand	364-371	8	8
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	406-424	19

Chain K: 15 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	66-70	5	9
α-helix	71-74	4
α-helix	75-79	5
β-strand	83	1	10
β-strand	87-89	3	11
β-strand	94-97	4	11
β-strand	117-121	5	11
β-strand	124-126	3	9
α-helix	132-138	7
α-helix	140-149	10
β-strand	153-158	6	9
α-helix	165-169	5
β-strand	171	1	12
β-strand	176	1	12
α-helix	178-189	12
β-strand	194	1	13
β-strand	200-204	5	14
β-strand	207-210	4	14
α-helix	213-228	16
β-strand	296	1	15
β-strand	298	1	13
β-strand	299-308	10	9
β-strand	311-314	4	9
α-helix	318-319	2
β-strand	328	1	9
β-strand	329-332	4	16
β-strand	338-341	4	16
β-strand	346-347	2	9
α-helix	351-363	13
β-strand	380-388	9	9
β-strand	391	1	15
β-strand	400-407	8	9
α-helix	408-409	2
α-helix	423-445	23
α-helix	458-460	3
α-helix	462-466	5
α-helix	468-472	5
β-strand	476-483	8	9
β-strand	486	1	10
α-helix	490-500	11
β-strand	503-508	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta-2B chain	B	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Kinesin-like protein KIF20A	K	protein	573	Mus musculus	P97329 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8F18_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>8F18_2 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (K), FASTA

>8F18_3 Kinesin-like protein KIF20A (chains K)
MSHRILSPPAGLLSDEDVVDSPILESTAADLRSVVRKDLLSDCSVISASLEDKQALLEDT
SEKVKVYLRIRPFLTSELDRQEDQGCVCIENTETLVLQAPKDSFALKSNERGVGQATHKF
TFSQIFGPEVGQVAFFNLTMKEMVKDVLKGQNWLIYTYGVTNSGKTYTIQGTSKDAGILP
QSLALIFNSLQGQLHPTPDLKPLLSNEVIWLDSKQIRQEEMKKLSLLIGGLQEEELSTSV
KKRVHTESRIGASNSFDSGVAGLSSTSQFTSSSQLDETSQLWAQPDTVPVSVPADIRFSV
WISFFEIYNELLYDLLEPPSHQHKRQTLRLCEDQNGNPYVKDLNWIHVRDVEEAWKLLKV
GRKNQSFASTHMNQQSSRSHSIFSIRILHLQGEGDIVPKISELSLCDLAGSERCKHQKSG
ERLKEAGNINTSLHTLGRCIAALRQNQQNRSKQNLIPFRDSKLTRVFQGFFTGRGRSCMI
VNVNPCASTYDETLHAAKFSALASQLVHAPPVHLGIPSLHSFIKKHSPQVGPGLEKEDKA
DSDLEDSPEDEADVSVYGKEELLQVLEHHHHHH

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
MG	Magnesium ion	Mg	1

Primary citation

Nucleotide-free structures of KIF20A illuminate atypical mechanochemistry in this kinesin-6. Ranaivoson, F.M., Crozet, V., Benoit, M.P.M.H. et al. Open Biol (2023) 13:230122-230122. DOI 10.1098/rsob.230122 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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