4HNA: Kinesin motor domain in the ADP-MG-ALFX state

Kinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN. Determined by X-ray diffraction at 3.19 Å resolution. Released 12 Jun 2013.

Method: X-ray diffraction
Resolution: 3.19 Å
Organisms: Ovis aries, ARTIFICIAL GENE, Homo sapiens
Chains: 4
Atoms: 10,607
Mol. weight: 159.18 kDa
Ligands: GTP, GDP, ADP, ALF
Released: 12 Jun 2013

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

Secondary structure: helices and β-sheets

4HNA contains 81 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: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	2
β-strand	61-63	3	2
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	150-161	12
β-strand	165-172	8	1
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	1
α-helix	206-217	12
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	285-287	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	3
α-helix	307-309	3
β-strand	312-321	10	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	352-356	5	3
α-helix	359-361	3
β-strand	368	1	4
α-helix	369-370	2
β-strand	373-381	9	3
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-434	20

Chain B: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-55	3	8
β-strand	60	1	7
β-strand	61-63	3	8
β-strand	65-69	5	5
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	5
α-helix	103-108	6
α-helix	110-127	18
β-strand	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
α-helix	183-197	15
β-strand	200-205	6	5
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	5
β-strand	269-273	5	9
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-321	10	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	373-381	9	9
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-437	23

Chain D: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	12-24	13
α-helix	27-35	9
α-helix	50-57	8
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-123	8
α-helix	126-134	9
α-helix	149-156	8
α-helix	159-166	8

Chain K: 18 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	10
α-helix	9	1
β-strand	10-15	6	11
α-helix	17-19	3
α-helix	20-23	4
β-strand	29	1	12
β-strand	32-34	3	13
β-strand	38-41	4	13
β-strand	44-47	4	13
β-strand	51-52	2	11
α-helix	58-65	8
α-helix	68-75	8
β-strand	79-85	7	11
β-strand	86	1	14
α-helix	91-95	5
β-strand	97	1	15
β-strand	105	1	15
α-helix	107-121	15
β-strand	126-138	13	11
β-strand	141-144	4	11
β-strand	153	1	11
β-strand	154-157	4	16
β-strand	163-166	4	16
β-strand	171-173	3	11
α-helix	176-187	12
β-strand	192-193	2	17
β-strand	201-202	2	17
β-strand	204-216	13	11
β-strand	222-231	10	11
α-helix	232-234	3
β-strand	235	1	14
α-helix	238-241	4
α-helix	246-270	25
α-helix	277-279	3
α-helix	282-285	4
α-helix	287-291	5
β-strand	295-302	8	11
β-strand	305	1	12
α-helix	306-308	3
α-helix	309-323	15
α-helix	325	1
β-strand	326	1	10
α-helix	327	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A	protein	451	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B	protein	445	Ovis aries	D0VWY9 (AlphaFold model)
Designed ankyrin repeat protein (DARPIN) D2	D	protein	169	ARTIFICIAL GENE
Kinesin-1 heavy chain	K	protein	349	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4HNA_1 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>4HNA_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (D), FASTA

>4HNA_3 DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2 (chains D)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNAEDDSGKTPLHLAAIKGHL
EIVEVLLKHGADVNAADKMGDTPLHLAALYGHLEIVEVLLKNGADVNATDTYGFTPLHLA
ADAGHLEIVEVLLKYGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Sequence of entity 4 (K), FASTA

>4HNA_4 Kinesin-1 heavy chain (chains K)
MADLAESNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQ
VYNDAAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVSSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNARTTIVI
CCSPSSYNESETKSTLLFGQRAKTIKNTVSVNVELTAEQWKKKYEKEKE

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
ALF	Tetrafluoroaluminate ion	Al F4	2
MG	Magnesium ion	Mg	3

Primary citation

Structure of a kinesin-tubulin complex and implications for kinesin motility. Gigant, B., Wang, W., Dreier, B. et al. Nat Struct Mol Biol (2013) 20:1001-1007. DOI 10.1038/nsmb.2624 · PubMed

Other PDB entries of the same protein (UniProt D0VWZ0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
9F07 2.21 Å, Tubulin:stathmin:darpin:tau MTBR3 complex
4DRX 2.22 Å, GTP-Tubulin in complex with a DARPIN
6TDE 2.29 Å, Tubulin-inhibitor complex
3RYI 2.4 Å, GDP-Tubulin: rb3 stathmin-like domain complex
5KX5 2.5 Å, Crystal structure of tubulin-stathmin-TTL-Compound 11 complex
3RYF 2.52 Å, GTP-Tubulin: RB3 Stathmin-like domain complex
4F6R 2.64 Å, Tubulin:Stathmin-like domain complex
6GVN 2.69 Å, Tubulin:TM-3 DARPin complex
3UT5 2.73 Å, Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
6H9B 2.75 Å, 1,1-Diheterocyclic Ethylenes Derived from Quinaldine and Carbazole as New Tubulin…

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