6JZD: Peptide-bound VASH2-SVBP complex

Crystal structure of peptide-bound VASH2-SVBP complex. Determined by X-ray diffraction at 2.48 Å resolution. Released 17 Jul 2019.

Method: X-ray diffraction
Resolution: 2.48 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 2,418
Mol. weight: 52.54 kDa
Released: 17 Jul 2019

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

Secondary structure: helices and β-sheets

6JZD contains 18 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: 17 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	77-85	9
α-helix	91-94	4
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
α-helix	260	1
β-strand	261	1	3
α-helix	262	1
β-strand	267-269	3	4
α-helix	271-273	3
α-helix	276-291	16
α-helix	295-297	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	27-59	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulinyl-Tyr carboxypeptidase 2	A	protein	355	Mus musculus	Q8C5G2 (AlphaFold model)
Small vasohibin-binding protein	B	protein	88	Homo sapiens	Q8N300 (AlphaFold model)
Glu-gly-glu-glu-tyr	C	protein	15	Mus musculus	P68369 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6JZD_1 Tubulinyl-Tyr carboxypeptidase 2 (chains A)
MTGSAADTHRCPHPKITKGTRSRSSHARPVSLATSGGSEEEDKDGGVLFHVNKSGFPIDS
HTWERMWLHVAKVHPRGGEMVGAIRNAAFLAKPSIPQVPNYRLSMTIPDWLQAIQNYMKT
LQYNHTGTQFFEIRKMRPLSGLMETAKEMTRESLPIKALEAVILGIYLTNGQPSIERFPI
SFKTYFSGNYFHHVVLGIYCNGYYGSLGMSRRAELMDKPLTFRTLSDLVFDFEDSYKKYL
HTVKKVKIGLYVPHEPHSFQPIEWKQLVLNVSKMLRADIRKELEKYARDMRMKILKPASA
HSPTQVRSRGKSLSPRRRQASPPRRLGRRDKSPALTEKKVADLGTLNEVGYQIRI

Sequence of entity 2 (B), FASTA

>6JZD_2 Small vasohibin-binding protein (chains B)
MHHHHHHHHHHSGDEVDAGSGHMDPPARKEKTKVKESVSRVEKAKQKSAQQELKQRQRAE
IYALNRVMTELEQQQFDEFCKQMQPPGE

Sequence of entity 3 (C), FASTA

>6JZD_3 GLU-GLY-GLU-GLU-TYR (chains C)
VDSVEGEGEEEGEEY

Primary citation

Structural basis of tubulin detyrosination by VASH2/SVBP heterodimer. Zhou, C., Yan, L., Zhang, W.H. et al. Nat Commun (2019) 10:3212-3212. DOI 10.1038/s41467-019-11277-8 · PubMed

Other PDB entries of the same protein (UniProt Q8C5G2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6JZC 2.2 Å, Structural basis of tubulin detyrosination
6JZE 2.51 Å, Crystal structure of VASH2-SVBP complex with the magic triangle I3C

Browse structure collections

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