4DRX: GTP-Tubulin

GTP-Tubulin in complex with a DARPIN. Determined by X-ray diffraction at 2.22 Å resolution. Released 11 Jul 2012.

Method: X-ray diffraction
Resolution: 2.22 Å
Organisms: Ovis aries, ARTIFICIAL GENE
Chains: 6
Atoms: 16,036
Mol. weight: 232.41 kDa
Ligands: GTP, MG
Released: 11 Jul 2012

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

Secondary structure: helices and β-sheets

4DRX contains 134 α-helices and 72 β-strands across 6 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: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
α-helix	10-27	18
β-strand	35	1	2
α-helix	49-51	3
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	73-76	4
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	206-216	11
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	4
β-strand	277	1	5
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	4
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-335	11
β-strand	343	1	4
α-helix	350-351	2
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	406-409	4
α-helix	416-435	20

Chain B: 29 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-46	4
α-helix	49-51	3
β-strand	53	1	8
β-strand	63	1	8
β-strand	65-69	5	6
α-helix	74-79	6
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	132-140	9	6
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	6
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	6
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	9
α-helix	276-277	2
α-helix	285-287	3
α-helix	288-293	6
α-helix	294-296	3
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
β-strand	373-381	9	9
α-helix	382-384	3
α-helix	385-401	17
α-helix	405-409	5
α-helix	415-437	23

Chain C: 28 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
β-strand	35	1	11
α-helix	49-51	3
β-strand	53-55	3	12
β-strand	60	1	11
β-strand	61-63	3	12
β-strand	65-69	5	10
α-helix	73-76	4
α-helix	89-91	3
β-strand	92-94	3	10
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	10
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	10
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	10
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
β-strand	269-273	5	13
β-strand	277	1	14
α-helix	285-287	3
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	13
α-helix	307-309	3
β-strand	312-321	10	13
α-helix	325-335	11
β-strand	343	1	13
β-strand	352-356	5	13
α-helix	359-361	3
β-strand	368	1	14
α-helix	369-370	2
β-strand	373-381	9	13
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	416-435	20

Chain D: 29 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	15
α-helix	10-27	18
β-strand	30	1	16
β-strand	35	1	17
β-strand	36	1	16
α-helix	41-46	4
α-helix	49-51	3
β-strand	53-55	3	18
β-strand	60	1	17
β-strand	61-63	3	18
β-strand	65-69	5	15
α-helix	74-79	6
α-helix	89-91	3
β-strand	92-94	3	15
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	132-140	9	15
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	15
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	15
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
α-helix	252-259	8
β-strand	267-268	2	15
β-strand	269-273	5	19
α-helix	276-277	2
α-helix	285-287	3
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	19
α-helix	307-309	3
β-strand	312-321	10	19
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	19
β-strand	351-356	6	19
β-strand	373-381	9	19
α-helix	382-384	3
α-helix	385-401	17
α-helix	405-409	5
α-helix	415-437	23

Chains E and 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	159-164	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	437	Ovis aries	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	431	Ovis aries	D0VWY9 (AlphaFold model)
Designed ankyrin repeat protein (DARPIN) D1	E, F	protein	169	ARTIFICIAL GENE

Sequence of entity 1 (A, C), FASTA

>4DRX_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGV

Sequence of entity 2 (B, D), FASTA

>4DRX_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAD

Sequence of entity 3 (E, F), FASTA

>4DRX_3 Designed ankyrin repeat protein (DARPIN) D1 (chains E, F)
MRGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHL
EIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLA
AIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4
MG	Magnesium ion	Mg	4

Primary citation

A designed ankyrin repeat protein selected to bind to tubulin caps the microtubule plus end. Pecqueur, L., Duellberg, C., Dreier, B. et al. Proc Natl Acad Sci U S A (2012) 109:12011-12016. DOI 10.1073/pnas.1204129109 · PubMed

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

5EYP 1.9 Å, Tubulin-darpin complex
3RYC 2.1 Å, Tubulin: RB3 stathmin-like domain complex
9F07 2.21 Å, Tubulin:stathmin:darpin:tau MTBR3 complex
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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