7ZCW: GMPCPP-microtubules

Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP. Determined by electron microscopy at 3.6 Å resolution. Released 14 Dec 2022.

Method: Electron microscopy
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 8
Atoms: 22,570
Mol. weight: 352.59 kDa
Ligands: G2P, MG, GTP
Released: 14 Dec 2022

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

Secondary structure: helices and β-sheets

7ZCW contains 153 α-helices and 118 β-strands across 8 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: 21 helices, 16 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	72-80	9
α-helix	89-91	3
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-125	14
β-strand	134-138	5	1
α-helix	145-160	16
β-strand	165-169	5	1
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-201	2	1
β-strand	203	1	4
α-helix	206-215	10
α-helix	224-238	15
α-helix	252-259	8
β-strand	269-273	5	4
α-helix	288-296	9
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-337	13
β-strand	343	1	4
β-strand	351-354	4	4
α-helix	359-360	2
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	405-409	5
α-helix	416-434	19

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-92	3	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	110-124	15
β-strand	130-138	9	5
α-helix	146-158	13
β-strand	163-170	8	5
α-helix	171-172	2
α-helix	181-192	12
β-strand	198-200	3	5
β-strand	202-203	2	5
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	8
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-268	2	8
β-strand	271	1	8
α-helix	277-279	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	349-354	6	8
β-strand	364-371	8	8
α-helix	375-389	15
α-helix	396-399	4
α-helix	406-424	19

Chain C: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	9
α-helix	60-73	14
α-helix	78-85	8
α-helix	91-94	4
α-helix	96-99	4
α-helix	107-120	14
β-strand	128-129	2	9
α-helix	139-152	14
α-helix	158-169	12
β-strand	177-186	10	10
β-strand	189-198	10	10
α-helix	200-202	3
β-strand	204-207	4	10
β-strand	217-222	6	10
α-helix	225-238	14
β-strand	242-248	7	10
α-helix	251-253	3
α-helix	260-263	4
β-strand	267-269	3	10
α-helix	276-291	16

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-52	26

Chain E: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	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	65-68	4	11
α-helix	74-79	6
β-strand	93	1	11
α-helix	103-104	2
α-helix	105-109	5
α-helix	115-127	13
β-strand	132-138	7	11
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-169	5	11
α-helix	172-174	3
α-helix	183-196	14
β-strand	200-202	3	11
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	14
α-helix	252-256	5
β-strand	269	1	15
β-strand	272-273	2	15
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	15
α-helix	325-336	12
β-strand	343	1	15
β-strand	351-354	4	15
β-strand	355	1	14
α-helix	359-361	3
β-strand	373-381	9	15
α-helix	384-399	16
α-helix	405-411	7
α-helix	416-434	19

Chain F: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	16
α-helix	10-28	19
β-strand	30	1	17
β-strand	36	1	17
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-54	4	18
β-strand	58-61	4	18
β-strand	63-66	4	16
α-helix	70-78	9
α-helix	87-89	3
β-strand	91	1	16
α-helix	103-107	5
α-helix	109-124	16
β-strand	130-138	9	16
α-helix	143-147	5
α-helix	148-158	11
β-strand	163	1	16
β-strand	165-170	6	16
α-helix	171-172	2
α-helix	181-192	12
β-strand	198-200	3	16
β-strand	202-203	2	16
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	19
α-helix	250-257	8
β-strand	265-266	2	16
β-strand	267-271	5	19
α-helix	286-293	8
α-helix	305-307	3
β-strand	310-318	9	19
α-helix	324-336	13
α-helix	338-340	3
β-strand	341	1	19
β-strand	349-354	6	19
β-strand	364-371	8	19
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-423	19

Chain G: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	20
α-helix	10-28	19
β-strand	30	1	21
β-strand	36	1	21
α-helix	41-45	5
α-helix	47-49	3
β-strand	51-54	4	22
β-strand	58-61	4	22
β-strand	63-66	4	20
α-helix	71-78	8
α-helix	87-89	3
β-strand	90-91	2	20
α-helix	103-107	5
α-helix	109-125	17
β-strand	130-138	9	20
α-helix	143-147	5
α-helix	148-158	11
β-strand	163	1	20
β-strand	166-169	4	20
α-helix	181-192	12
β-strand	199-200	2	20
β-strand	202	1	20
α-helix	204-210	7
α-helix	211-215	5
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	23
α-helix	250-257	8
β-strand	265-266	2	20
β-strand	267-268	2	23
β-strand	271	1	23
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-319	10	23
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	23
β-strand	349-354	6	23
β-strand	363-371	9	23
α-helix	372-374	3
α-helix	375-389	15
α-helix	396-399	4
α-helix	406-423	18

Chain H: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	24
α-helix	10-28	19
β-strand	30	1	25
β-strand	36	1	25
α-helix	42-45	4
α-helix	47-49	3
β-strand	51-53	3	26
β-strand	59-61	3	26
β-strand	63-67	5	24
α-helix	70-78	9
α-helix	87-89	3
β-strand	91-92	2	24
α-helix	103-107	5
α-helix	108-125	18
β-strand	130-138	9	24
α-helix	143-148	6
α-helix	149-158	10
β-strand	163-170	8	24
α-helix	171-172	2
α-helix	181-192	12
β-strand	198-203	6	24
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
α-helix	238-240	3
β-strand	246	1	27
α-helix	250-257	8
β-strand	265-266	2	24
β-strand	267-268	2	27
β-strand	271	1	27
α-helix	276-278	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-318	9	27
α-helix	324-336	13
α-helix	338-340	3
β-strand	341	1	27
β-strand	349-354	6	27
β-strand	364-371	8	27
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-399	4
α-helix	405-424	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, E	protein	451	Homo sapiens	P68363 (AlphaFold model)
Tubulin beta-2B chain	B, F, G, H	protein	445	Homo sapiens	Q9BVA1 (AlphaFold model)
Tubulinyl-Tyr carboxypeptidase 2	C	protein	355	Homo sapiens	Q86V25 (AlphaFold model)
Small vasohibin-binding protein	D	protein	73	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>7ZCW_1 Tubulin alpha-1B chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, F, G, H), FASTA

>7ZCW_2 Tubulin beta-2B chain (chains B, F, G, H)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEEGEDEA

Sequence of entity 3 (C), FASTA

>7ZCW_3 Tubulinyl-Tyr carboxypeptidase 2 (chains C)
MTGSAADTHRCPHPKGAKGTRSRSSHARPVSLATSGGSEEEDKDGGVLFHVNKSGFPIDS
HTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKT
LQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKALEAVILGIYLTNGQPSIERFPI
SFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTLSDLIFDFEDSYKKYL
HTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILKPASA
HSPTQVRSRGKSLSPRRRQASPPRRLGRREKSPALPEKKVADLSTLNEVGYQIRI

Sequence of entity 4 (D), FASTA

>7ZCW_4 Small vasohibin-binding protein (chains D)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGEKHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
G2P	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	4
MG	Magnesium ion	Mg	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

VASH1-SVBP and VASH2-SVBP generate different detyrosination profiles on microtubules. Ramirez-Rios, S., Choi, S.R., Sanyal, C. et al. J Cell Biol (2023) 222. DOI 10.1083/jcb.202205096 · PubMed

Other PDB entries of the same protein (UniProt P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule

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