7CNO: Phomopsin A

Phomopsin A in complex with tubulin. Determined by X-ray diffraction at 2.5 Å resolution. Released 4 Aug 2021.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Sus scrofa, Mus musculus, Gallus gallus
Chains: 6
Atoms: 18,166
Mol. weight: 266.33 kDa
Ligands: GTP, MG, CA, GDP
Released: 4 Aug 2021

Explore 7CNO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CNO contains 129 α-helices and 94 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	10-28	19
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	73-79	7
α-helix	89-91	3
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	110-112	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	284-287	4
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	359-361	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	415-436	22

Chain B: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	6
α-helix	10-27	18
β-strand	30	1	7
β-strand	35	1	8
β-strand	36	1	7
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-55	3	9
β-strand	60	1	8
β-strand	61-63	3	9
β-strand	65-69	5	6
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	6
α-helix	103-108	6
α-helix	110-127	18
β-strand	134-140	7	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	224-243	20
α-helix	252-259	8
β-strand	267-268	2	6
β-strand	269-273	5	10
α-helix	285-287	3
α-helix	288-296	9
α-helix	298-300	3
β-strand	301	1	10
α-helix	307-309	3
β-strand	312-321	10	10
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	10
β-strand	351-356	6	10
α-helix	359-360	2
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-435	21

Chain C: 31 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	11
α-helix	10-28	19
β-strand	35	1	12
α-helix	48-51	4
β-strand	53-55	3	13
β-strand	60	1	12
β-strand	61-63	3	13
β-strand	65-69	5	11
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	11
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	11
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-172	8	11
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	11
α-helix	206-216	11
α-helix	224-243	20
α-helix	252-259	8
α-helix	268	1
β-strand	269-273	5	14
β-strand	277	1	15
α-helix	278-281	4
α-helix	285-287	3
α-helix	288-294	7
α-helix	298-300	3
β-strand	301	1	14
α-helix	307-309	3
β-strand	312-321	10	14
α-helix	325-338	14
β-strand	343	1	14
β-strand	352-356	5	14
α-helix	359-360	2
β-strand	368	1	15
α-helix	369-370	2
β-strand	373-381	9	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-434	20
α-helix	438-439	2

Chain D: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	16
α-helix	10-27	18
β-strand	30	1	17
β-strand	35	1	18
β-strand	36	1	17
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-57	5	18
β-strand	60-63	4	18
β-strand	65-69	5	16
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	16
α-helix	103-108	6
α-helix	110-127	18
β-strand	132-140	9	16
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	16
α-helix	183-197	15
β-strand	200-205	6	16
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
α-helix	252-259	8
β-strand	267-268	2	16
β-strand	269-273	5	19
α-helix	288-295	8
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
α-helix	359-360	2
β-strand	373-381	9	19
α-helix	382-384	3
α-helix	385-399	15
α-helix	406-409	4
α-helix	415-437	23

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	4
β-strand	17-25	9	4
α-helix	47-141	95

Chain G: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	20
α-helix	12-23	12
β-strand	27-29	3	20
β-strand	39-41	3	20
α-helix	49-51	3
β-strand	61-62	2	20
α-helix	69-72	4
α-helix	74-83	10
β-strand	97-100	4	21
α-helix	128-140	13
β-strand	147-150	4	21
β-strand	161-163	3	21
α-helix	166-173	8
β-strand	180-184	5	21
β-strand	189	1	22
β-strand	192	1	23
β-strand	197-207	11	23
β-strand	213-216	4	23
β-strand	220-227	8	23
α-helix	228	1
α-helix	243-249	7
α-helix	258-260	3
β-strand	261-262	2	23
α-helix	264-270	7
α-helix	271-275	5
α-helix	279	1
α-helix	280-284	5
α-helix	285-302	18
β-strand	310-311	2	20
β-strand	313-321	9	23
β-strand	322	1	22
β-strand	327-333	7	23
α-helix	340-342	3
α-helix	343-349	7
α-helix	350-355	6
β-strand	375-377	3	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D	protein	445	Sus scrofa	A0A8D1UIR5 (AlphaFold model)
Stathmin-4	E	protein	143	Mus musculus	P63042 (AlphaFold model)
Tubulin tyrosine ligase	G	protein	384	Gallus gallus	A0A8V0Z8P0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7CNO_1 Tubulin alpha-1B chain (chains A, C)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D), FASTA

>7CNO_2 Tubulin beta chain (chains B, D)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM
AACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (E), FASTA

>7CNO_3 Stathmin-4 (chains E)
MADMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRRDPSLEEIQKKLEAAEERRK
YQEAELLKHLAEKREHEREVIQKAIEENNNFIKMAKEKLAQKMESNKENREAHLAAMLER
LQEKDKHAEEVRKNKELKEEASR

Sequence of entity 4 (G), FASTA

>7CNO_4 Tubulin tyrosine ligase (chains G)
MYTFVVRDENSSVYAEVSRLLLATGQWKRLRKDNPRFNLMLGERNRLPFGRLGHEPGLVQ
LVNYYRGADKLCRKASLVKLIKTSPELSESCTWFPESYVIYPTNLKTPVAPAQNGIRHLI
NNTRTDEREVFLAAYNRRREGREGNVWIAKSSAGAKGEGILISSEASELLDFIDEQGQVH
VIQKYLEKPLLLEPGHRKFDIRSWVLVDHLYNIYLYREGVLRTSSEPYNSANFQDKTCHL
TNHCIQKEYSKNYGRYEEGNEMFFEEFNQYLMDALNTTLENSILLQIKHIIRSCLMCIEP
AISTKHLHYQSFQLFGFDFMVDEELKVWLIEVNGAPACAQKLYAELCQGIVDVAISSVFP
LADTGQKTSQPTSIFIKLHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	4
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
HOS	Phomopsin A	C36 H45 Cl N6 O12	2
ACP	Phosphomethylphosphonic acid adenylate ester	C11 H18 N5 O12 P3	1

Water and common crystallization additives (CL, MES) are not listed.

Primary citation

The high-resolution X-ray structure of vinca-domain inhibitors of microtubules provides a rational approach for drug design. Chengyong, W., Jinghong, X., Yanyan, W. et al. FEBS Lett (2021) 595:195-205. DOI 10.1002/1873-3468.14003 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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