6J4Q: Tubulinyl-Tyr carboxypeptidase 2

Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and functional implications. Determined by X-ray diffraction at 2.7 Å resolution. Released 1 May 2019.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 9,379
Mol. weight: 151.15 kDa
Ligands: TQ8
Released: 1 May 2019

Explore 6J4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J4Q contains 57 α-helices and 44 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: 13 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	79-85	7
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
α-helix	213-215	3
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
α-helix	262-263	2
β-strand	267-269	3	4
α-helix	276-291	16

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-58	30

Chain C: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	5
α-helix	60-73	14
α-helix	77-85	9
α-helix	91-94	4
α-helix	96-99	4
α-helix	107-121	15
β-strand	123	1	6
β-strand	128-129	2	5
α-helix	139-152	14
β-strand	156	1	6
α-helix	158-169	12
β-strand	175-186	12	7
β-strand	189-200	12	7
β-strand	204-207	4	7
α-helix	213-215	3
β-strand	218-222	5	7
α-helix	225-238	14
β-strand	242-248	7	7
β-strand	267-270	4	7
α-helix	271-273	3
α-helix	276-292	17

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-56	30

Chain F: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	8
α-helix	58-59	2
α-helix	60-73	14
α-helix	80-85	6
α-helix	93-99	7
α-helix	107-121	15
β-strand	123	1	9
β-strand	128-129	2	8
β-strand	138	1	10
α-helix	139-152	14
β-strand	156	1	9
α-helix	158-168	11
β-strand	176-186	11	11
β-strand	189-200	12	11
β-strand	203-207	5	11
α-helix	213-215	3
β-strand	218-222	5	11
α-helix	225-237	13
α-helix	241	1
β-strand	242-248	7	11
α-helix	250-253	4
α-helix	260	1
β-strand	261	1	10
α-helix	262	1
β-strand	267-269	3	11
α-helix	271-273	3
α-helix	276-291	16

Chain G: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	29-54	26

Chain J: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	50-51	2	12
α-helix	58-59	2
α-helix	60-73	14
α-helix	79-85	7
α-helix	91-94	4
α-helix	96-99	4
α-helix	107-121	15
β-strand	123	1	13
β-strand	128-129	2	12
α-helix	139-152	14
β-strand	156	1	13
α-helix	158-169	12
β-strand	176-185	10	14
β-strand	190-200	11	14
β-strand	203-207	5	14
α-helix	213-215	3
β-strand	218-222	5	14
α-helix	225-238	14
α-helix	241	1
β-strand	242-248	7	14
α-helix	256-257	2
α-helix	260-262	3
β-strand	267-270	4	14
α-helix	276-291	16

Chain K: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	31-56	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 2	A, C, F, J	protein	251	Homo sapiens	Q86V25 (AlphaFold model)
Small vasohibin-binding protein	B, D, G, K	protein	66	Homo sapiens	Q8N300 (AlphaFold model)

Sequence of entity 1 (A, C, F, J), FASTA

>6J4Q_1 Tubulinyl-Tyr carboxypeptidase 2 (chains A, C, F, J)
GVLFHVNKSGFPIDSHTWERMWMHVAKVHPKGGEMVGAIRNAAFLAKPSIPQVPNYRLSM
TIPDWLQAIQNYMKTLQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKCLEAVILG
IYLTNGQPSIERFPISFKTYFSGNYFHHVVLGIYCNGRYGSLGMSRRAELMDKPLTFRTL
SDLIFDFEDSYKKYLHTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEK
YARDMRMKILK

Sequence of entity 2 (B, D, G, K), FASTA

>6J4Q_2 Small vasohibin-binding protein (chains B, D, G, K)
MDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAEIYALNRVMTELEQQQFDEFCKQ
MQPPGE

Ligands and cofactors

ID	Name	Formula	Copies
TQ8	N-[(2S)-4-chloro-3-oxo-1-phenyl-butan-2-yl]-4-methyl-benzenesulfonamide	C17 H18 Cl N O3 S	6

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
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
6J4O 2.3 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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