6J4V: Tubulinyl-Tyr carboxypeptidase 2

Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications. Determined by X-ray diffraction at 2.1 Å resolution. Released 1 May 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 2,621
Mol. weight: 40.01 kDa
Ligands: PO4
Released: 1 May 2019

Explore 6J4V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J4V contains 13 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: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	1
α-helix	58-59	2
α-helix	60-73	14
α-helix	77-84	8
α-helix	96-99	4
α-helix	107-121	15
β-strand	123	1	2
β-strand	128-129	2	1
β-strand	138	1	3
α-helix	139-152	14
β-strand	156	1	2
α-helix	158-169	12
β-strand	176-186	11	4
β-strand	189-200	12	4
β-strand	203-207	5	4
β-strand	218-222	5	4
α-helix	225-238	14
α-helix	241	1
β-strand	242-248	7	4
α-helix	250-253	4
β-strand	261	1	3
β-strand	267-269	3	4
α-helix	271-273	3
α-helix	276-292	17

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	25-57	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 2	A	protein	251	Homo sapiens	Q86V25 (AlphaFold model)
Small vasohibin-binding protein	B	protein	66	Homo sapiens	Q8N300 (AlphaFold model)
Tubulin alpha-1B chain	C	protein	21	Homo sapiens	P68363 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J4V_1 Tubulinyl-Tyr carboxypeptidase 2 (chains A)
GVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSM
TIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILG
IYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTL
SDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEK
YARDMRMKILK

Sequence of entity 2 (B), FASTA

>6J4V_2 Small vasohibin-binding protein (chains B)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFSKQ
MQPPGE

Sequence of entity 3 (C), FASTA

>6J4V_3 Tubulin alpha-1B chain (chains C)
DYEEVGVDSVEGEGEEEGECY

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (GOL) are not listed.

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 Q86V25 (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…
6QBY 2.09 Å, Crystal structure of VASH 2 in complex with SVBP
6J4O 2.3 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4Q 2.7 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4S 2.8 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
7ZCW 3.6 Å, Cryo-EM structure of GMPCPP-microtubules in complex with VASH2-SVBP

Browse structure collections

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