6OJQ: Tubulin beta-2B chain

Monomeric kinesin-1 motor domain in no-nucleotide state bound to GMPCPP-stabilized microtubule. Determined by electron microscopy at 3.67 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 3.67 Å
Organisms: Bos taurus, Homo sapiens
Chains: 3
Atoms: 9,177
Mol. weight: 133.03 kDa
Ligands: G2P, MG, GTP
Released: 15 Apr 2020

Explore 6OJQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6OJQ contains 60 α-helices and 73 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: 24 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	7
β-strand	6-9	4	8
α-helix	10-27	18
α-helix	49-51	3
β-strand	53	1	9
β-strand	63	1	9
β-strand	65-68	4	8
α-helix	72-80	9
α-helix	82-84	3
β-strand	92	1	8
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-126	12
β-strand	131-132	2	7
β-strand	134-136	3	10
β-strand	137-138	2	8
β-strand	140	1	11
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-168	4	10
β-strand	171-172	2	11
α-helix	183-196	14
β-strand	200-201	2	10
β-strand	204-205	2	11
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	12
α-helix	252-259	8
β-strand	269-273	5	13
α-helix	278-283	6
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312	1	14
β-strand	314-318	5	13
β-strand	320-321	2	15
α-helix	325-337	13
β-strand	343	1	14
β-strand	351-354	4	13
β-strand	355	1	12
α-helix	358-360	3
β-strand	373-374	2	15
β-strand	375-380	6	13
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22

Chain B: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	11-28	18
β-strand	30	1	2
β-strand	35	1	3
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	72-80	9
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	105-109	5
α-helix	110-127	18
β-strand	132-138	7	1
β-strand	140	1	1
α-helix	145-160	16
β-strand	165	1	1
β-strand	167-172	6	1
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-205	6	1
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	4
α-helix	252-257	6
β-strand	267-268	2	1
β-strand	269-273	5	5
α-helix	279-281	3
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	5
α-helix	307-309	3
β-strand	312-318	7	5
β-strand	320	1	6
α-helix	325-338	14
β-strand	343	1	5
β-strand	351-354	4	5
β-strand	355	1	4
β-strand	374	1	6
β-strand	375-381	7	5
α-helix	384-399	16
α-helix	405-411	7
α-helix	415-434	20

Chain K: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	16
α-helix	16-18	3
α-helix	20-23	4
β-strand	29	1	17
β-strand	32-34	3	18
β-strand	38-41	4	18
β-strand	44-47	4	18
β-strand	50-52	3	16
α-helix	58-65	8
α-helix	67-73	7
β-strand	79-84	6	16
α-helix	91-95	5
β-strand	97-98	2	19
β-strand	105	1	19
α-helix	108-119	12
β-strand	126	1	20
β-strand	129-137	9	16
β-strand	138	1	21
β-strand	141	1	21
β-strand	142	1	22
β-strand	153	1	22
β-strand	154-156	3	23
β-strand	164-166	3	23
β-strand	171-172	2	16
α-helix	176-188	13
β-strand	192	1	24
β-strand	202	1	24
β-strand	205-215	11	16
β-strand	216	1	20
β-strand	222-231	10	16
α-helix	238-241	4
α-helix	246-269	24
α-helix	277-279	3
α-helix	281-284	4
β-strand	296-302	7	16
β-strand	305	1	17
α-helix	306-308	3
α-helix	309-323	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin beta-2B chain	B	protein	426	Bos taurus	Q6B856 (AlphaFold model)
Tubulin alpha-1B chain	A	protein	437	Bos taurus	P81947 (AlphaFold model)
Kinesin-1 heavy chain	K	protein	317	Homo sapiens	P33176 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6OJQ_1 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQ

Sequence of entity 2 (A), FASTA

>6OJQ_2 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGV

Sequence of entity 3 (K), FASTA

>6OJQ_3 Kinesin-1 heavy chain (chains K)
NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDAAK
KIVKDVLEGYNGTIFAYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLE
FHIKVSYFEIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGATERFVSSPDEVMDTIDEGK
SNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAV
LDEAKNINKSLSALGNVISALAEGSTYVPYRDSKMTRILQDSLGGNARTTIVICCSPSSY
NESETKSTLLFGQRAKT

Ligands and cofactors

ID	Name	Formula	Copies
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Primary citation

Structural Intermediates of the Dimeric Kinesin Stepping Cycle Revealed by Cryo-EM. Cha, H.K., Debs, G., Liu, X. et al. To be published.

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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