2IBF: Human vinculin's head domain

Human vinculin's head domain (Vh1, residues 1-258) in complex with two vinculin binding sites of Shigella flexneri's IpaA (residues 565-587). Determined by X-ray diffraction at 3.2 Å resolution. Released 18 Sept 2007.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Homo sapiens, Shigella flexneri
Chains: 3
Atoms: 2,359
Mol. weight: 35.53 kDa
Released: 18 Sept 2007

Explore 2IBF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IBF contains 9 α-helices and 0 β-strands across 3 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	7-29	23
α-helix	43-64	22
α-helix	68-97	30
α-helix	102-147	46
α-helix	154-181	28
α-helix	185-215	31
α-helix	224-250	27

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	566-582	17

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	569-584	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A	protein	266	Homo sapiens	P18206 (AlphaFold model)
Invasin ipaA	B, D	protein	25	Shigella flexneri	P18010 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2IBF_1 Vinculin (chains A)
MEHHHHHHMPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVS
NLVRVGKETVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGS
RGILSGTSDLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMA
KMIDERQQELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNF
TVEKMSAEINEIIRVLQLTSWDEDAW

Sequence of entity 2 (B, D), FASTA

>2IBF_2 Invasin ipaA (chains B, D)
NHAIYEKAKEVSSALSKVLSKIDDT

Primary citation

Vinculin binding in its closed conformation by a helix addition mechanism. Nhieu, G.T., Izard, T. EMBO J (2007) 26:4588-4596. DOI 10.1038/sj.emboj.7601863 · 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
1YDI 1.8 Å, Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's…
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

Browse structure collections

About this viewer

MolViewer shows 2IBF 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.