7X4N: C. elegans kinesin-4 KLP-12

Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin. Determined by X-ray diffraction at 2.88 Å resolution. Released 21 Sept 2022.

Method: X-ray diffraction
Resolution: 2.88 Å
Organisms: Sus scrofa, synthetic construct, Caenorhabditis elegans
Chains: 4
Atoms: 10,394
Mol. weight: 158.36 kDa
Ligands: GTP, MG, ANP, GDP
Released: 21 Sept 2022

Explore 7X4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7X4N contains 67 α-helices and 60 β-strands across 4 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: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	1
α-helix	10-27	18
β-strand	35	1	2
α-helix	38-40	3
β-strand	53-55	3	3
β-strand	60	1	2
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-126	12
β-strand	134-140	7	1
α-helix	144-157	14
β-strand	165-172	8	1
α-helix	175-177	3
α-helix	183-195	13
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-238	15
α-helix	241-243	3
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	285-287	3
α-helix	288-293	6
α-helix	294-296	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312	1	6
β-strand	316-321	6	4
α-helix	325-338	14
β-strand	343	1	6
β-strand	352-355	4	4
α-helix	359-361	3
β-strand	368	1	5
β-strand	373-379	7	4
β-strand	381	1	6
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-435	21

Chain B: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	7
α-helix	10-28	19
β-strand	30	1	8
β-strand	36	1	8
α-helix	47-49	3
β-strand	51-53	3	9
β-strand	59-61	3	9
β-strand	63-67	5	7
α-helix	70-72	3
α-helix	87-89	3
β-strand	90-92	3	7
α-helix	101-105	5
α-helix	116-125	10
β-strand	130-138	9	7
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-169	7	7
β-strand	170	1	10
α-helix	181-195	15
β-strand	198-200	3	7
β-strand	203	1	10
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
α-helix	250-257	8
β-strand	265-266	2	7
β-strand	267-271	5	11
α-helix	289-293	5
α-helix	296-298	3
β-strand	299	1	11
α-helix	305-307	3
β-strand	310-319	10	11
α-helix	325-336	12
β-strand	341	1	11
β-strand	349-354	6	11
β-strand	363-371	9	11
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-425	21

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	2-11	10
α-helix	15-22	8
α-helix	38-44	7
α-helix	48-55	8
α-helix	71-78	8
α-helix	81-89	9
α-helix	104-110	7
α-helix	114-122	9

Chain E: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	12
α-helix	13-16	4
α-helix	17-21	5
β-strand	26	1	13
β-strand	28-29	2	14
β-strand	36-39	4	14
β-strand	43-46	4	14
β-strand	49-51	3	12
α-helix	57-64	8
α-helix	66-73	8
β-strand	78-84	7	12
β-strand	85	1	15
α-helix	90-94	5
α-helix	111-127	17
β-strand	139-149	11	12
β-strand	154-156	3	12
β-strand	169-172	4	16
β-strand	178-181	4	16
β-strand	186-187	2	12
α-helix	191-202	12
β-strand	207-210	4	17
β-strand	213-217	5	17
β-strand	220-230	11	12
β-strand	252-253	2	12
β-strand	256-261	6	12
α-helix	262-264	3
β-strand	265	1	15
α-helix	268-271	4
α-helix	276-297	22
α-helix	310-312	3
α-helix	314-318	5
α-helix	320-324	5
β-strand	328-335	8	12
β-strand	338	1	13
α-helix	342-355	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1A chain	A	protein	451	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)
DARPin	C	protein	159	synthetic construct
Kinesin-like protein	E	protein	365	Caenorhabditis elegans	G5EGS3 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7X4N_1 Tubulin alpha-1A chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRAHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>7X4N_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (C), FASTA

>7X4N_3 DARPin (chains C)
DLGKKLLEAARAGQDDEVRVLMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGAD
VSASDLMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLRLAAVMGHLKIVEAL
LKHGADVNAQDKFGKTAYDTSIDNGSEDLAEILQKLNLE

Sequence of entity 4 (E), FASTA

>7X4N_4 Kinesin-like protein (chains E)
MADTCVQVALRIRPQGNREKLEGSRVCTSVLPNDPQVTIGGDRSFTYDHVFDMPTLQYVV
YESCVEKLVDGLFDGYNATVLAYGQTGSGKTHTMGTAFDAAVTQKEEDLGVIPRAIQHTF
RKIAECKAQAIEQGLLEPAFEVSVQFVELYNDDVLDLLSDDRSMSSSIRIHEDSRGEIVL
HGVEQRSVFDMHGTMDILKNGALNRTVAATNMNEQSSRSHAIFTLHLKQQRVAANPLDES
GEQKTGELEMEMLCAKFHFVDLAGSERMKRTGATGDRAKEGISINVGLLALGNVIAALGG
ANGKVSHVPYRDSKLTRLLQDSLGGNSRTLMIACCSPSDSDFVETLNTMKYANRAKEIKN
KVVAN

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex. Taguchi, S., Nakano, J., Imasaki, T. et al. Elife (2022) 11. DOI 10.7554/eLife.77877 · PubMed

Other PDB entries of the same protein (UniProt P02550 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T1D 2.9 Å, Cryo-EM reconstruction of undecorated GDP microtubule
6MZG 3.21 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
7U0F 3.53 Å, HIV-1 Rev in complex with tubulin
8QAU 3.54 Å, Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
8X9P 3.54 Å, HURP (428-534)-alpha-tubulin-beta-tubulin complex
6MZE 3.6 Å, Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with…
6KIQ 3.62 Å, Complex of yeast cytoplasmic dynein MTBD-High and MT with DTT
1TUB 3.7 Å, Tubulin alpha-beta dimer, electron diffraction
9EDT 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
9EEB 3.7 Å, Tubulin cofactors D,E,G bound to tubulin dimer
9EDR 3.8 Å, Tubulin Cofactors D,E,G,C and Tubulin complex -- TBCC N Terminus Bound to Tubulin
9EDS 3.8 Å, Tubulin cofactors D,E,G,C bound to tubulin dimer -- TBCC N terminus unbound

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