3RYH: GMPCPP-Tubulin: RB3 Stathmin-like domain complex

GMPCPP-Tubulin: RB3 Stathmin-like domain complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 5 Oct 2011.

Method: X-ray diffraction
Resolution: 2.8 Å
Organisms: OVIS ARIES, Rattus norvegicus
Chains: 5
Atoms: 15,107
Mol. weight: 220.2 kDa
Ligands: GTP, MG, G2P
Released: 5 Oct 2011

Explore 3RYH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RYH contains 112 α-helices and 73 β-strands across 5 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	10-28	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	111-125	15
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
α-helix	268	1
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	325-338	14
β-strand	343	1	4
β-strand	349-356	8	4
α-helix	359-360	2
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	415-435	21
α-helix	438-439	2

Chain B: 28 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	41-47	5
α-helix	49-51	3
β-strand	53-55	3	8
α-helix	56	1
β-strand	61-63	3	8
β-strand	65-69	5	6
α-helix	73-79	7
α-helix	84-86	3
β-strand	92-94	3	6
α-helix	103-108	6
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	175-177	3
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	288-293	6
α-helix	298-300	3
β-strand	301	1	9
α-helix	307-309	3
β-strand	312-320	9	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	374-381	8	9
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-437	23

Chain C: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	10
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	11
β-strand	61-63	3	11
β-strand	65-69	5	10
α-helix	72-78	7
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	150-161	12
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
β-strand	248	1	12
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	12
β-strand	277	1	13
α-helix	288-293	6
α-helix	294-296	3
α-helix	298-300	3
β-strand	301	1	12
β-strand	312-321	10	12
α-helix	325-336	12
β-strand	343	1	12
β-strand	351-356	6	12
α-helix	359-361	3
β-strand	368	1	13
α-helix	369-370	2
β-strand	373-381	9	12
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	416-436	21

Chain D: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	14
α-helix	10-27	18
β-strand	30	1	15
β-strand	35	1	16
β-strand	36	1	15
α-helix	41-47	5
α-helix	49-51	3
β-strand	53-54	2	17
β-strand	60	1	16
β-strand	62-63	2	17
β-strand	65-69	5	14
α-helix	73-79	7
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	14
α-helix	103-108	6
α-helix	110-127	18
β-strand	134-140	7	14
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	14
α-helix	173	1
α-helix	183-197	15
β-strand	200-205	6	14
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	14
β-strand	269-273	5	18
α-helix	285-287	3
α-helix	288-293	6
α-helix	298-300	3
β-strand	301	1	18
α-helix	307-309	3
β-strand	312-321	10	18
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	18
β-strand	351-356	6	18
α-helix	359-360	2
β-strand	373-381	9	18
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-437	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-14	8	4
β-strand	17-25	9	4
α-helix	47-138	92

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha chain	A, C	protein	451	OVIS ARIES	D0VWZ0 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	OVIS ARIES	D0VWY9 (AlphaFold model)
Stathmin-4	E	protein	143	Rattus norvegicus	P63043 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3RYH_1 Tubulin alpha chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>3RYH_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVATIFRGRMSMKEVDEQMLNIQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>3RYH_3 Stathmin-4 (chains E)
XADMEVIELNKATSGQSWEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	4
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	2

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

Primary citation

The Determinants That Govern Microtubule Assembly from the Atomic Structure of GTP-Tubulin. Nawrotek, A., Knossow, M., Gigant, B. J Mol Biol (2011) 412:35-42. DOI 10.1016/j.jmb.2011.07.029 · 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
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…

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