4ATX: Tubulin beta-2B chain

Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin dimer, modelled into the 8A cryo-EM map of doublecortin- microtubules decorated with kinesin. Determined by electron microscopy at 8.2 Å resolution. Released 26 Sept 2012.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: BOS TAURUS, RATTUS NORVEGICUS
Chains: 3
Atoms: 9,183
Mol. weight: 139.25 kDa
Ligands: GDP, GTP
Released: 26 Sept 2012

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

Secondary structure: helices and β-sheets

4ATX contains 55 α-helices and 48 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: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	6-9	4	1
α-helix	12-26	15
β-strand	30	1	2
β-strand	36	1	2
α-helix	49-52	4
β-strand	55	1	3
β-strand	61	1	3
β-strand	65-69	5	1
α-helix	72-78	7
α-helix	83-85	3
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-139	6	1
α-helix	144-148	5
α-helix	149-160	12
β-strand	165-170	6	1
α-helix	184-194	11
β-strand	200-202	3	1
α-helix	206-214	9
α-helix	224-242	19
β-strand	248	1	4
α-helix	252-259	8
β-strand	267-268	2	1
β-strand	269-271	3	4
α-helix	289-295	7
α-helix	307-309	3
β-strand	312-320	9	4
α-helix	325-338	14
β-strand	351-356	6	4
β-strand	375-381	7	4
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-436	22

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	5
α-helix	10-26	17
β-strand	65-69	5	5
α-helix	73-78	6
β-strand	92-94	3	5
α-helix	103-107	5
α-helix	109-128	20
β-strand	134-139	6	5
α-helix	144-149	6
α-helix	150-160	11
β-strand	165	1	5
β-strand	167-170	4	5
α-helix	184-194	11
β-strand	200-203	4	5
α-helix	206-215	10
α-helix	224-242	19
α-helix	252-259	8
β-strand	269-271	3	5
β-strand	277	1	6
α-helix	284-287	4
α-helix	288-294	7
α-helix	298-300	3
β-strand	312-321	10	5
α-helix	325-336	12
β-strand	343	1	5
β-strand	351-355	5	5
β-strand	368	1	6
β-strand	373-381	9	5
α-helix	382-384	3
α-helix	385-399	15
α-helix	403-405	3
α-helix	406-409	4
α-helix	415-429	15
α-helix	431-434	4

Chain C: 14 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	7
α-helix	16-18	3
α-helix	20-25	6
β-strand	32-34	3	8
β-strand	38-41	4	8
β-strand	44-47	4	8
β-strand	50-52	3	7
α-helix	58-65	8
α-helix	67-75	9
β-strand	79-84	6	7
α-helix	91-95	5
β-strand	97	1	9
β-strand	105	1	9
α-helix	107-122	16
β-strand	126-138	13	7
β-strand	141-144	4	7
β-strand	153	1	7
β-strand	155-157	3	10
β-strand	163-165	3	10
β-strand	171-172	2	7
α-helix	176-191	16
α-helix	197-203	7
β-strand	205-216	12	7
β-strand	222-231	10	7
α-helix	232-234	3
α-helix	256-270	15
α-helix	277-279	3
α-helix	281-286	6
β-strand	295-302	8	7
α-helix	310-320	11
α-helix	325-328	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-2B chain	A	protein	445	BOS TAURUS	Q6B856 (AlphaFold model)
Tubulin alpha-1D chain	B	protein	452	BOS TAURUS	Q2HJ86 (AlphaFold model)
Kinesin-1 heavy chain	C	protein	340	RATTUS NORVEGICUS	Q2PQA9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4ATX_1 TUBULIN BETA-2B CHAIN (chains A)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 2 (B), FASTA

>4ATX_2 TUBULIN ALPHA-1D CHAIN (chains B)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEEGEEY

Sequence of entity 3 (C), FASTA

>4ATX_3 KINESIN-1 HEAVY CHAIN (chains C)
MADPAECNIKVMCRFRPLNESEVNRGDKYVAKFQGEDTVMIASKPYAFDRVFQSSTSQEQ
VYNDCAKKIVKDVLEGYNGTIFAYGQTSSGKNHTMEGKLHDPEGMGIIPRIVQDIFNYIY
SMDENLEFHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVM
DTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSK
TGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNCRTTIVI
CCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTAEQW

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Molecular Basis for Specific Regulation of Neuronal Kinesin- 3 Motors by Doublecortin Family Proteins. Liu, J.S., Schubert, C.R., Fu, X. et al. Mol Cell (2012) 47:707. DOI 10.1016/J.MOLCEL.2012.06.025 · PubMed

Other PDB entries of the same protein (UniProt Q6B856 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8K 1.52 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
8QL2 1.7 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
6ZWB 1.75 Å, Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
4I4T 1.8 Å, Crystal structure of tubulin-RB3-TTL-Zampanolide complex
5IYZ 1.8 Å, Tubulin-MMAE complex
5NQU 1.8 Å, Tubulin Darpin cryo structure
7YZ3 1.8 Å, Molecular snapshots of drug release from tubulin: Apo state
8QEA 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL3 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL4 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL5 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL6 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…

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