6WSL: VASH1-SVBP

Cryo-EM structure of VASH1-SVBP bound to microtubules. Determined by electron microscopy at 3.1 Å resolution. Released 26 Aug 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 18,204
Mol. weight: 278.63 kDa
Ligands: G2P, GTP
Released: 26 Aug 2020

Explore 6WSL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WSL contains 113 α-helices and 96 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: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	1
β-strand	6-9	4	2
α-helix	11-26	16
β-strand	53-55	3	3
β-strand	61-63	3	3
β-strand	65-69	5	2
α-helix	72-78	7
β-strand	93-94	2	2
α-helix	104	1
α-helix	105-109	5
α-helix	111-123	13
β-strand	132-137	6	1
β-strand	140	1	1
α-helix	145-160	16
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	185-196	12
β-strand	201-204	4	1
α-helix	207-210	4
α-helix	230-238	9
β-strand	246	1	4
β-strand	269-273	5	4
α-helix	288-294	7
β-strand	312	1	5
β-strand	316-317	2	6
β-strand	319-321	3	4
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	5
α-helix	344	1
β-strand	352-353	2	6
β-strand	356	1	4
α-helix	358-360	3
β-strand	373-379	7	4
α-helix	384-386	3
α-helix	388-399	12
α-helix	406-409	4
α-helix	417-434	18

Chain B: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	7
α-helix	12-17	6
α-helix	21-27	7
β-strand	30	1	8
β-strand	36	1	8
α-helix	41-43	3
β-strand	51	1	9
β-strand	61	1	9
β-strand	63-67	5	7
α-helix	72-77	6
β-strand	90-92	3	7
α-helix	102-105	4
α-helix	109-111	3
α-helix	113-123	11
β-strand	129-135	7	7
β-strand	138	1	10
α-helix	143-158	16
β-strand	163-166	4	7
β-strand	169-170	2	10
α-helix	181-188	8
α-helix	190-193	4
β-strand	198-200	3	7
β-strand	202-203	2	10
α-helix	205-209	5
α-helix	210-214	5
α-helix	225-234	10
α-helix	250-256	7
β-strand	265-266	2	7
β-strand	267-271	5	11
α-helix	279-283	5
α-helix	290-293	4
α-helix	305-307	3
β-strand	310-317	8	11
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	11
β-strand	349-352	4	11
β-strand	359	1	12
β-strand	361	1	12
β-strand	365-371	7	11
α-helix	375-391	17
α-helix	396-399	4
α-helix	406-422	17

Chain C: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	74-76	3
α-helix	77-80	4
α-helix	91-93	3
α-helix	107-109	3
α-helix	118-129	12
α-helix	130-132	3
α-helix	151-154	4
α-helix	158-161	4
α-helix	169-178	10
β-strand	187-196	10	13
β-strand	201-211	11	13
β-strand	214-218	5	13
α-helix	224-226	3
β-strand	233	1	13
α-helix	237-249	13
β-strand	253-259	7	13
α-helix	261-264	4
β-strand	278-281	4	13
α-helix	287-290	4
α-helix	293-304	12

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
α-helix	36-50	15

Chain E: 22 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
β-strand	6-8	3	15
α-helix	11-26	16
β-strand	53-55	3	16
β-strand	61-63	3	16
β-strand	65-67	3	15
β-strand	68-69	2	17
α-helix	72-78	7
β-strand	93-94	2	17
α-helix	104	1
α-helix	105-109	5
α-helix	111-123	13
β-strand	132	1	14
β-strand	134-137	4	18
β-strand	138	1	15
β-strand	140	1	18
α-helix	144-146	3
α-helix	148-160	13
β-strand	165-171	7	18
α-helix	172-174	3
α-helix	185-194	10
β-strand	201-204	4	18
α-helix	228-238	11
β-strand	246	1	19
α-helix	256-258	3
β-strand	269	1	20
β-strand	272-273	2	21
α-helix	288-293	6
α-helix	294-296	3
β-strand	312	1	22
β-strand	316-317	2	23
β-strand	319-321	3	21
α-helix	325-336	12
α-helix	342	1
β-strand	343	1	22
α-helix	344	1
β-strand	352-353	2	23
β-strand	356	1	19
α-helix	358-360	3
β-strand	373-376	4	21
β-strand	379	1	20
α-helix	382-387	6
α-helix	389-399	11
α-helix	406-409	4
α-helix	415-417	3
α-helix	418-434	17

Chain F: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	24
α-helix	12-15	4
α-helix	21-27	7
α-helix	41-44	4
β-strand	51	1	25
β-strand	54	1	26
β-strand	56	1	26
β-strand	61	1	25
β-strand	63-67	5	24
α-helix	72-77	6
α-helix	87-89	3
β-strand	90-92	3	24
α-helix	102-105	4
α-helix	110-125	16
β-strand	129-135	7	24
β-strand	138	1	27
α-helix	147-158	12
β-strand	163-166	4	24
β-strand	169-170	2	27
α-helix	181-188	8
α-helix	190-193	4
β-strand	198-199	2	24
β-strand	202-203	2	27
α-helix	205-209	5
α-helix	210-214	5
α-helix	225-234	10
α-helix	250-256	7
β-strand	267-271	5	28
α-helix	290-293	4
α-helix	305-307	3
β-strand	310-317	8	28
α-helix	323-336	14
β-strand	341	1	28
β-strand	349-352	4	28
β-strand	359	1	29
β-strand	361	1	29
β-strand	365-371	7	28
α-helix	375-391	17
α-helix	396-399	4
α-helix	406-422	17

Chain G: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	74-76	3
α-helix	77-80	4
α-helix	91-93	3
α-helix	107-109	3
α-helix	118-129	12
α-helix	130-132	3
α-helix	150-161	12
α-helix	169-178	10
β-strand	187-196	10	30
β-strand	201-211	11	30
β-strand	214-218	5	30
α-helix	224-226	3
β-strand	233	1	30
α-helix	236-248	13
β-strand	253-259	7	30
α-helix	261-264	4
β-strand	278-281	4	30
α-helix	287-304	18

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
α-helix	37-50	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1A chain	A, E	protein	451	Homo sapiens	Q71U36 (AlphaFold model)
Tubulin beta-3 chain	B, F	protein	450	Homo sapiens	Q13509 (AlphaFold model)
Tubulinyl-Tyr carboxypeptidase 1	C, G	protein	259	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	D, H	protein	66	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6WSL_1 Tubulin alpha-1A chain (chains A, E)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, F), FASTA

>6WSL_2 Tubulin beta-3 chain (chains B, F)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPK

Sequence of entity 3 (C, G), FASTA

>6WSL_3 Tubulinyl-Tyr carboxypeptidase 1 (chains C, G)
DLRDGGVPFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPT
FQPSTPVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLE
AVILGIYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPP
AFRTLSELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFR
KELERHARDMRLKIGKGTG

Sequence of entity 4 (D, H), FASTA

>6WSL_4 Small vasohibin-binding protein (chains D, H)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGE

Ligands and cofactors

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

Primary citation

Cryo-EM structure of VASH1-SVBP bound to microtubules. Li, F., Li, Y., Ye, X. et al. Elife (2020) 9. DOI 10.7554/eLife.58157 · PubMed

Other PDB entries of the same protein (UniProt Q71U36 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9WD9 2.26 Å, GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
6J8F 2.28 Å, Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin
9WD7 2.34 Å, GMPCPP-stabilizsd human alpha1A/beta3 microtubule
9WDA 2.35 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 microtubule
9WDB 2.39 Å, Paclitaxel/GMPCPP-stabilized human alpha1A/beta3 S239C microtubule
22AK 2.41 Å, GDP human alpha1A/beta3 microtubule
22AJ 2.48 Å, GDP human alpha1A/beta3 S239C microtubule
9OX7 2.69 Å, In situ microtubule structure in the axon of a human neuron
8SH7 2.8 Å, TUBB4B and TUBA1A Heterodimer from Human Respiratory Doublet Microtubules
7UNG 3.6 Å, 48-nm repeat of the human respiratory doublet microtubule
5JCO 4.0 Å, Structure and dynamics of single-isoform recombinant neuronal human tubulin
8J07 4.1 Å, 96nm repeat of human respiratory doublet microtubule and associated axonemal complexes

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