8QEA: Tubulin alpha-1B chain

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 96 fs structure. Determined by X-ray diffraction at 1.8 Å resolution. Released 11 Sept 2024.

Method: X-ray diffraction
Resolution: 1.8 Å
Organisms: Bos taurus, synthetic construct
Chains: 3
Atoms: 8,998
Mol. weight: 119.73 kDa
Ligands: GTP, MG, CA, IBL
Released: 11 Sept 2024

Explore 8QEA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QEA contains 63 α-helices and 35 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: 27 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	73-78	6
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	206-217	12
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	283-287	5
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-336	12
β-strand	343	1	4
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	405-409	5
α-helix	416-435	20

Chain B: 26 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-54	4	8
β-strand	58-61	4	8
β-strand	63-67	5	6
α-helix	71-77	7
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-106	6
α-helix	108-125	18
β-strand	132-138	7	6
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-170	8	6
α-helix	171	1
α-helix	181-195	15
β-strand	198-203	6	6
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	9
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	9
α-helix	305-307	3
β-strand	310-319	10	9
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	9
β-strand	349-354	6	9
α-helix	357-358	2
β-strand	363-371	9	9
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-427	23

Chain F: 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	60-67	8
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	451	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B	protein	445	Bos taurus	Q6B856 (AlphaFold model)
Designed Ankyrin Repeat Protein (DARPIN) D1	F	protein	169	synthetic construct

Sequence of entity 1 (A), FASTA

>8QEA_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>8QEA_2 Tubulin beta-2B chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (F), FASTA

>8QEA_3 Designed Ankyrin Repeat Protein (DARPIN) D1 (chains F)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHL
EIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLA
AIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
CA	Calcium ion	Ca	1
IBL	Azo-Combretastatin A4 (cis)	C16 H18 N2 O5	1

Primary citation

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution. Weinert, T., Wranik, M., Seidel, H.-P. et al. To be published.

Other PDB entries of the same protein (UniProt P81947 (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
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:…
8QL7 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…

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