6J8F: Small vasohibin-binding protein

Crystal structure of SVBP-VASH1 with peptide mimic the C-terminal of alpha-tubulin. Determined by X-ray diffraction at 2.28 Å resolution. Released 19 Jun 2019.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,185
Mol. weight: 33.99 kDa
Released: 19 Jun 2019

Explore 6J8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J8F contains 13 α-helices and 10 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: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-46	20

Chain B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	71-84	14
α-helix	88-96	9
α-helix	102-110	9
α-helix	118-132	15
β-strand	134	1	1
β-strand	149	1	2
α-helix	150-163	14
β-strand	167	1	1
α-helix	169-180	12
β-strand	187-197	11	3
β-strand	200-211	12	3
β-strand	214-218	5	3
α-helix	224-226	3
β-strand	229-233	5	3
α-helix	236-249	14
β-strand	253-259	7	3
α-helix	261-264	4
β-strand	272	1	2
α-helix	273	1
β-strand	278-281	4	3
α-helix	282-285	4
α-helix	287-301	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Small vasohibin-binding protein	A	protein	46	Homo sapiens	Q8N300 (AlphaFold model)
Tubulinyl-Tyr carboxypeptidase 1	B	protein	238	Homo sapiens	Q7L8A9 (AlphaFold model)
8-mer peptide	C	protein	8	Homo sapiens	Q71U36 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J8F_1 Small vasohibin-binding protein (chains A)
PPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTE

Sequence of entity 2 (B), FASTA

>6J8F_2 Tubulinyl-Tyr carboxypeptidase 1 (chains B)
MDEATWERMWKHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPSTPVPERLEAVQRY
IRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILGIYLTNSMPTLER
FPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTLSELVLDFEAAYG
RCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELERHARDMRLKIG

Sequence of entity 3 (C), FASTA

>6J8F_3 8-mer peptide (chains C)
GEEEGECY

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 Q8N300 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6J4P 1.6 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J7B 1.62 Å, Crystal structure of VASH1-SVBP in complex with epoY
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
6QBY 2.09 Å, Crystal structure of VASH 2 in complex with SVBP
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6NVQ 2.1 Å, Crystal structure of the VASH1-SVBP complex
6OCF 2.1 Å, The crystal structure of VASH1-SVBP complex
6JZC 2.2 Å, Structural basis of tubulin detyrosination

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