5EYP: Tubulin-darpin complex

Tubulin-darpin complex. Determined by X-ray diffraction at 1.9 Å resolution. Released 20 Jul 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Ovis aries, synthetic construct
Chains: 3
Atoms: 8,501
Mol. weight: 120.57 kDa
Ligands: LOC, GDP, MG, GTP
Released: 20 Jul 2016

Explore 5EYP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5EYP contains 64 α-helices and 36 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: 31 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	150-160	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	206-215	10
α-helix	224-244	21
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	3
β-strand	277	1	4
α-helix	284-287	4
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	3
β-strand	312-321	10	3
α-helix	325-338	14
α-helix	342	1
β-strand	343	1	3
α-helix	344	1
α-helix	350-351	2
β-strand	352-356	5	3
α-helix	359-360	2
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	416-435	20

Chain B: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	35	1	7
β-strand	36	1	6
α-helix	41-45	3
α-helix	49-51	3
β-strand	53-56	4	7
β-strand	60-63	4	7
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	110-128	19
β-strand	132-140	9	5
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	5
β-strand	174	1	8
β-strand	177	1	8
α-helix	183-197	15
β-strand	200-205	6	5
α-helix	206-217	12
α-helix	224-238	15
α-helix	240-243	4
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	385-400	16
α-helix	405-409	5
α-helix	415-437	23

Chain F: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	14-24	11
α-helix	27-35	9
α-helix	50-56	7
α-helix	60-68	9
α-helix	83-90	8
α-helix	93-101	9
α-helix	116-122	7
α-helix	126-134	9

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)	F	protein	169	synthetic construct

Sequence of entity 1 (A), FASTA

>5EYP_1 Tubulin alpha chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B), FASTA

>5EYP_2 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (F), FASTA

>5EYP_3 DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) (chains F)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRVLMANGADVNATDASGLTPLHLAATYGHL
EIVEVLLKHGADVSASDLMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLRLA
AVMGHLKIVEALLKHGADVNAQDKFGKTAYDTSIDNGSEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
LOC	N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethana…	C22 H25 N O6	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1

Water and common crystallization additives (GOL, SO4) are not listed.

Primary citation

Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Ahmad, S., Pecqueur, L., Dreier, B. et al. Sci Rep (2016) 6:28922-28922. DOI 10.1038/srep28922 · PubMed

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

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…
3RYH 2.8 Å, GMPCPP-Tubulin: RB3 Stathmin-like domain complex

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