1YDI: Human Vinculin Head Domain

Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's Vinculin-Binding Site (Residues 731-760). Determined by X-ray diffraction at 1.8 Å resolution. Released 19 Jul 2005.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,725
Mol. weight: 32.43 kDa
Released: 19 Jul 2005

Explore 1YDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YDI contains 10 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: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	7-25	19
α-helix	41-64	24
α-helix	68-97	30
α-helix	102-147	46
α-helix	148-150	3
α-helix	154-181	28
β-strand	182	1	1
α-helix	185-216	32
α-helix	224-248	25
α-helix	253-255	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	743-763	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
vinculin isoform VCL	A	protein	263	Homo sapiens	P18206 (AlphaFold model)
Alpha-actinin 4	B	protein	24	Homo sapiens	O43707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1YDI_1 vinculin isoform VCL (chains A)
HHHHHMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLV
RVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGI
LSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMI
DERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVE
KMSAEINEIIRVLQLTSWDEDAW

Sequence of entity 2 (B), FASTA

>1YDI_2 Alpha-actinin 4 (chains B)
VGWEQLLTTIARTINEVENQILTR

Primary citation

Structural Dynamics of {alpha}-Actinin-Vinculin Interactions. Bois, P.R., Borgon, R.A., Vonrhein, C. et al. Mol Cell Biol (2005) 14:6112-6122. DOI 10.1128/MCB.25.14.6112-6122.2005 · PubMed

Other PDB entries of the same protein (UniProt P18206 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LN2 1.0 Å, The second SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
4LNP 1.41 Å, The first SH3 domain from CAP/Ponsin in complex with proline rich peptide from Vinculin
3RF3 1.61 Å, Shigella IpaA-VBS3 in complex with human vinculin
3S90 1.97 Å, Human vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33;…
3TJ5 1.99 Å, human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding…
3MYI 2.2 Å, Human metavinculin tail domain
4DJ9 2.25 Å, Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin…
1RKE 2.35 Å, Human vinculin head (1-258) in complex with human vinculin tail (879-1066)
1SYQ 2.42 Å, Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin…
5L0I 2.45 Å, Human metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134)
3VF0 2.54 Å, Raver1 in complex with metavinculin L954 deletion mutant
9QWO 2.54 Å, Vinculin tail bound to paxillin LD2

Browse structure collections

About this viewer

MolViewer shows 1YDI 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.