6J4U: Tubulinyl-Tyr carboxypeptidase 1

Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications. Determined by X-ray diffraction at 2.0 Å resolution. Released 1 May 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,489
Mol. weight: 36.86 kDa
Released: 1 May 2019

Explore 6J4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J4U contains 16 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: 15 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	62	1	1
α-helix	69-70	2
α-helix	71-84	14
α-helix	88-95	8
α-helix	101-103	3
α-helix	105-110	6
α-helix	118-132	15
β-strand	134	1	2
β-strand	140	1	1
α-helix	150-163	14
β-strand	167	1	2
α-helix	169-180	12
β-strand	186-197	12	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
α-helix	252	1
β-strand	253-259	7	3
α-helix	260-264	5
α-helix	271-273	3
β-strand	278-281	4	3
α-helix	282-285	4
α-helix	287-303	17

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	26-49	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 1	A	protein	251	Homo sapiens	Q7L8A9 (AlphaFold model)
Small vasohibin-binding protein	B	protein	66	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J4U_1 Tubulinyl-Tyr carboxypeptidase 1 (chains A)
GVPFFVNRGGLPVDSHTWERMWMHVAKIHPDGEKVAQRIRGATDLPKIPIPSVPTFQPST
PVPERLEAVQRYIRELQYNHTGTQFFEIKKSRPLTGLMDLAKEMTKEALPIKCLEAVILG
IYLTNSMPTLERFPISFKTYFSGNYFRHIVLGVNFAGRYGALGMSRREDLMYKPPAFRTL
SELVLDFEAAYGRCWHVLKKVKLGQSVSHDPHSVEQIEWKHSVLDVERLGRDDFRKELER
HARDMRLKIGK

Sequence of entity 2 (B), FASTA

>6J4U_2 Small vasohibin-binding protein (chains B)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGE

Primary citation

Structural basis of tubulin detyrosination by the vasohibin-SVBP enzyme complex. Wang, N., Bosc, C., Ryul Choi, S. et al. Nat Struct Mol Biol (2019) 26:571-582. DOI 10.1038/s41594-019-0241-y · PubMed

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

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
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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