9GNQ: Microtubule-associated Kif5B IAK tail mutant

Microtubule-associated Kif5B IAK tail mutant bound to ADP. Determined by electron microscopy at 2.9 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 3
Atoms: 9,309
Mol. weight: 147.16 kDa
Ligands: ADP, MG, GTP, TA1
Released: 20 Nov 2024

Explore 9GNQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9GNQ contains 60 α-helices and 49 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: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	53-55	3	6
β-strand	61-63	3	6
β-strand	65-69	5	5
α-helix	74-79	6
β-strand	92-94	3	5
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-127	13
β-strand	132-138	7	5
α-helix	145-160	16
β-strand	165-171	7	5
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	5
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	7
α-helix	278-281	4
α-helix	288-294	7
β-strand	312-321	10	7
α-helix	325-337	13
β-strand	343	1	7
β-strand	351-356	6	7
α-helix	359-362	4
β-strand	373-381	9	7
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	416-436	21

Chain B: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
β-strand	30	1	2
β-strand	36	1	2
α-helix	41-47	5
α-helix	49-51	3
β-strand	53-56	4	3
β-strand	60-63	4	3
β-strand	65-69	5	1
α-helix	72-79	8
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	132-140	9	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-171	7	1
α-helix	172-173	2
α-helix	183-197	15
β-strand	200-204	5	1
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-242	3
β-strand	248	1	4
α-helix	252-259	8
β-strand	267-268	2	1
β-strand	269-273	5	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	312-321	10	4
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	4
β-strand	351-356	6	4
α-helix	359-360	2
β-strand	373-381	9	4
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-434	20

Chain K: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	8
α-helix	17-19	3
α-helix	20-22	3
β-strand	32-34	3	9
β-strand	38-40	3	9
β-strand	45-47	3	9
β-strand	50-51	2	8
α-helix	58-65	8
α-helix	67-73	7
β-strand	79-85	7	8
α-helix	91-94	4
β-strand	97	1	10
β-strand	105	1	10
α-helix	108-119	12
β-strand	126-137	12	8
β-strand	142-144	3	8
β-strand	153	1	8
β-strand	154-156	3	11
β-strand	164-166	3	11
β-strand	171-173	3	8
α-helix	176-187	12
β-strand	192-193	2	12
β-strand	201-202	2	12
β-strand	205-216	12	8
β-strand	222-231	10	8
α-helix	232-235	4
α-helix	238-240	3
α-helix	246-269	24
α-helix	277-279	3
α-helix	281-285	5
α-helix	287-290	4
β-strand	295-301	7	8
α-helix	306-308	3
α-helix	309-322	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)
Tubulin alpha-1B chain	A	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Kinesin-1 heavy chain	K	protein	408	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9GNQ_1 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 2 (A), FASTA

>9GNQ_2 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (K), FASTA

>9GNQ_3 Kinesin-1 heavy chain (chains K)
MADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQ
VYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVI
CCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTAEQWKKKYEKEKEKNKILRNTTGS
TGSTGSTGSTGSTGSTGSTGSTGSARRGHSATGSTSGTPGQHPAASPT

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail. Atherton, J., Chegkazi, M.S., Leusciatti, M. et al. Nat Commun (2025) 16:6214-6214. DOI 10.1038/s41467-025-61498-3 · PubMed

Other PDB entries of the same protein (UniProt P02554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5XP3 2.3 Å, Crystal structure of apo T2R-TTL
6XES 2.32 Å, Tubulin-RB3_SLD in complex with compound 40a
7EMJ 2.33 Å, Crystal structure of T2R-TTL-Barbigerone complex
7XQY 2.35 Å, Crystal structure of T2R-TTL-15 complex
7EXC 2.39 Å, Crystal structure of T2R-TTL-1129A2 complex
6LS4 2.4 Å, A novel anti-tumor agent S-40 in complex with tubulin

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