5Y04: Vinculin

Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin. Determined by X-ray diffraction at 2.85 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 2.85 Å
Organism: Mus musculus
Chains: 2
Atoms: 2,233
Mol. weight: 39.51 kDa
Released: 28 Mar 2018

Explore 5Y04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Y04 contains 11 α-helices and 2 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: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	7-29	23
α-helix	35-38	4
α-helix	41-64	24
α-helix	68-97	30
α-helix	104-146	43
α-helix	159-179	21
β-strand	182	1	1
α-helix	185-210	26
α-helix	225-249	25

Chain B: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	309-314	6
α-helix	329-352	24
α-helix	360-368	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A	protein	252	Mus musculus	Q64727 (AlphaFold model)
Catenin alpha-1	B	protein	102	Mus musculus	P26231 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5Y04_1 Vinculin (chains A)
GPMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVG
KETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSG
TSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDER
QQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMS
AEINEIIRVLQL

Sequence of entity 2 (B), FASTA

>5Y04_2 Catenin alpha-1 (chains B)
GPGELAYALNNFDKQIIVDPLSFSEERFRPSLEERLESIISGAALMADSSCTRDDRRERI
VAECNAVRQALQDLLSEYMGNAGRKERSDALNSAIDKMTKKT

Primary citation

The force-sensing device region of alpha-catenin is an intrinsically disordered segment in the absence of intramolecular stabilization of the autoinhibitory form. Hirano, Y., Amano, Y., Yonemura, S. et al. Genes Cells (2018) 23:370-385. DOI 10.1111/gtc.12578 · PubMed

Other PDB entries of the same protein (UniProt Q64727 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SR0 1.49 Å, Mouse vinculin head domain 1 (VD1) (residues 2-258) with A50I mutation in complex with…

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