3ZDL: Vinculin head

Vinculin head (1-258) in complex with a RIAM fragment. Determined by X-ray diffraction at 2.3 Å resolution. Released 13 Feb 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: GALLUS GALLUS, HOMO SAPIENS
Chains: 2
Atoms: 2,261
Mol. weight: 34.87 kDa
Released: 13 Feb 2013

Explore 3ZDL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZDL contains 13 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: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	5	1	1
α-helix	6-26	21
α-helix	29-32	4
α-helix	35-36	2
α-helix	40-63	24
α-helix	67-96	30
α-helix	101-146	46
α-helix	147-149	3
α-helix	153-180	28
β-strand	181	1	1
α-helix	184-216	33
α-helix	222-246	25
α-helix	252-254	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A	protein	280	GALLUS GALLUS	P12003 (AlphaFold model)
Amyloid beta A4 precursor protein-binding family B member 1-interacting protein	B	protein	32	HOMO SAPIENS	Q7Z5R6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3ZDL_1 VINCULIN (chains A)
MGSSHHHHHHSSGLVPRGSHMMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPD
LTAPVSAVQAAVSNLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADP
YSVPARDYLIDGSRGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVT
YTKNLGPGMTKMAKMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTK
SQGIEEALKNRNFTVEKMSAEINEIIRVLQLTSWDEDAWA

Sequence of entity 2 (B), FASTA

>3ZDL_2 AMYLOID BETA A4 PRECURSOR PROTEIN-BINDING FAMILY B MEMBER 1-INTERACTING PROTEIN (chains B)
MGESSEDIDQMFSTLLGEMDLLTQSLGVDTLY

Primary citation

Riam and Vinculin Binding to Talin are Mutually Exclusive and Regulate Adhesion Assembly and Turnover. Goult, B.T., Zacharchenko, T., Bate, N. et al. J Biol Chem (2013) 288:8238. DOI 10.1074/JBC.M112.438119 · PubMed

Other PDB entries of the same protein (UniProt P12003 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QKR 1.8 Å, Crystal structure of the vinculin tail and a pathway for activation
1ZVZ 1.8 Å, Vinculin Head (0-258) in Complex with the Talin Rod Residue 820-844
1T01 2.06 Å, Vinculin complexed with the VBS1 helix from talin
1ZW2 2.1 Å, Vinculin Head (0-258) in Complex with the Talin Rod residues 2345-2369
4E17 2.3 Å, Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin
1U6H 2.38 Å, Vinculin head (0-258) in complex with the talin vinculin binding site 2 (849-879)
4E18 2.4 Å, Alpha-E-catenin is an autoinhibited molecule that co-activates vinculin
1XWJ 2.6 Å, Vinculin head (1-258) in complex with the talin vinculin binding site 3 (1945-1969)
2GDC 2.74 Å, Structure of Vinculin VD1 / IpaA560-633 complex
6FQ4 2.89 Å, Structure of Chlamydial virulence factor TarP and vinculin head domain
6NR7 3.0 Å, Rerefinement of chicken vinculin
1ST6 3.1 Å, Crystal structure of a cytoskeletal protein

Browse structure collections

About this viewer

MolViewer shows 3ZDL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.