4LNU: Nucleotide-free kinesin motor domain

Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin. Determined by X-ray diffraction at 2.19 Å resolution. Released 3 Dec 2014.

Method: X-ray diffraction
Resolution: 2.19 Å
Organisms: Ovis aries, Artificial gene, Homo sapiens
Chains: 4
Atoms: 11,209
Mol. weight: 157.23 kDa
Ligands: GDP, MG, GTP
Released: 3 Dec 2014

Explore 4LNU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LNU contains 79 α-helices and 57 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: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
β-strand	35	1	2
α-helix	48-51	4
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	73-80	8
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	134-140	7	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	284-286	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
β-strand	312-321	10	4
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	4
α-helix	344	1
β-strand	352-356	5	4
α-helix	359-361	3
β-strand	368	1	5
α-helix	369-370	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	416-435	20

Chain B: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	10-28	19
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	41-43	3
α-helix	49-51	3
β-strand	53-56	4	8
β-strand	60-63	4	8
β-strand	65-69	5	6
α-helix	74-80	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-108	6
α-helix	110-127	18
β-strand	134-140	7	6
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	9
α-helix	280-282	3
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	9
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	9
β-strand	351-356	6	9
α-helix	359-360	2
β-strand	374-381	8	9
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-437	22

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9
α-helix	149-155	7
α-helix	159-166	8

Chain K: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	10
α-helix	16-19	4
α-helix	20-23	4
β-strand	32-34	3	11
β-strand	38-40	3	11
β-strand	41	1	12
β-strand	44	1	12
β-strand	47	1	11
β-strand	50-52	3	10
α-helix	58-62	5
α-helix	63-67	5
α-helix	68-74	7
β-strand	79-84	6	10
α-helix	91-95	5
β-strand	97	1	13
β-strand	105	1	13
α-helix	108-118	11
β-strand	126-138	13	10
β-strand	141-144	4	10
β-strand	153	1	10
β-strand	154-157	4	14
β-strand	163-166	4	14
β-strand	171-172	2	10
α-helix	176-187	12
β-strand	192	1	15
β-strand	202	1	15
β-strand	205-216	12	10
β-strand	222-232	11	10
α-helix	233-235	3
α-helix	245-269	25
α-helix	277-279	3
α-helix	281-285	5
α-helix	287-290	4
β-strand	295-302	8	10
α-helix	309-322	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A	protein	451	Ovis aries	A0A836D7T3 (AlphaFold model)
Tubulin beta chain	B	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Designed ankyrin repeat protein (DARPIN) D1	D	protein	169	Artificial gene
Kinesin-1 heavy chain	K	protein	325	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4LNU_1 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>4LNU_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSIHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (D), FASTA

>4LNU_3 Designed ankyrin repeat protein (DARPIN) D1 (chains D)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHL
EIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLA
AIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Sequence of entity 4 (K), FASTA

>4LNU_4 Kinesin-1 heavy chain (chains K)
MADLAESNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQ
VYNDAAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVSSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNARTTIVI
CCSPSSYNESETKSTLLFGQRAKTI

Ligands and cofactors

ID	Name	Formula	Copies
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

Water and common crystallization additives (MES, SO4, GOL) are not listed.

Primary citation

The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement. Cao, L., Wang, W., Jiang, Q. et al. Nat Commun (2014) 5:5364-5364. DOI 10.1038/ncomms6364 · PubMed

Other PDB entries of the same protein (UniProt A0A836D7T3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TH4 2.12 Å, Tubulin-inhibitor complex
7Q1F 2.35 Å, CPAP:TUBULIN:IE5 alpharep complex
7Z0F 2.4 Å, Cpap:s-TUBULIN:IIH5 alpharep complex
8CGZ 2.53 Å, tubulin-AB8939 complex
7Q1E 2.7 Å, CPAP:TUBULIN:IIH5 alpharep complex
7Z0G 3.49 Å, CPAP:TUBULIN:IE5 alpharep complex P1 space group

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