6J7B: VASH1-SVBP

Crystal structure of VASH1-SVBP in complex with epoY. Determined by X-ray diffraction at 1.62 Å resolution. Released 19 Jun 2019.

Method: X-ray diffraction
Resolution: 1.62 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,700
Mol. weight: 35.36 kDa
Ligands: BJL
Released: 19 Jun 2019

Explore 6J7B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J7B contains 15 α-helices and 12 β-strands across 2 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: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	61-62	2	1
α-helix	69-70	2
α-helix	71-84	14
α-helix	88-95	8
α-helix	101-110	10
α-helix	118-132	15
β-strand	134	1	2
β-strand	139-140	2	1
β-strand	149	1	3
α-helix	150-163	14
β-strand	167	1	2
α-helix	169-178	10
β-strand	186-197	12	4
β-strand	200-211	12	4
β-strand	214-218	5	4
α-helix	224-226	3
β-strand	229-233	5	4
α-helix	236-249	14
α-helix	252	1
β-strand	253-259	7	4
α-helix	260-264	5
α-helix	271	1
β-strand	272	1	3
α-helix	273	1
β-strand	278-281	4	4
α-helix	282-303	22

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	21-51	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 1	A	protein	250	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	B	protein	52	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J7B_1 Tubulinyl-Tyr carboxypeptidase 1 (chains A)
GVPFFVNRGGLPVDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPST
PVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILG
IYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTL
SELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELER
HARDMRLKIG

Sequence of entity 2 (B), FASTA

>6J7B_2 Small vasohibin-binding protein (chains B)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQ

Ligands and cofactors

ID	Name	Formula	Copies
BJL	N-[(3R)-4-ethoxy-3-hydroxy-4-oxobutanoyl]-L-tyrosine	C15 H19 N O7	1

Primary citation

Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. Liao, S., Rajendraprasad, G., Wang, N. et al. Cell Res (2019) 29:533-547. DOI 10.1038/s41422-019-0187-y · PubMed

Other PDB entries of the same protein (UniProt Q7L8A9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OCG 1.83 Å, Crystal structure of VASH1-SVBP complex bound with EpoY
6J8O 1.85 Å, Structure of a hypothetical protease
6J8N 1.95 Å, Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1
6J4U 2.0 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6OCH 2.0 Å, Crystal structure of VASH1-SVBP complex bound with parthenolide
6NVQ 2.1 Å, Crystal structure of the VASH1-SVBP complex
6OCF 2.1 Å, The crystal structure of VASH1-SVBP complex
6K81 2.28 Å, Crystal structure of human VASH1-SVBP complex
6J8F 2.28 Å, Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin
6LPG 2.3 Å, human VASH1-SVBP complex
6J9H 2.31 Å, Crystal structure of SVBP-VASH1 complex
6WSL 3.1 Å, Cryo-EM structure of VASH1-SVBP bound to microtubules

Browse structure collections

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