2GDC: Vinculin VD1 / IpaA560-633 complex

Structure of Vinculin VD1 / IpaA560-633 complex. Determined by X-ray diffraction at 2.74 Å resolution. Released 8 Aug 2006.

Method: X-ray diffraction
Resolution: 2.74 Å
Organisms: Gallus gallus, Shigella flexneri
Chains: 2
Atoms: 2,006
Mol. weight: 31.89 kDa
Released: 8 Aug 2006

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

Secondary structure: helices and β-sheets

2GDC contains 9 α-helices and 0 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, 0 β-strands

Element	Residues	Length
α-helix	7-19	13
α-helix	41-64	24
α-helix	68-97	30
α-helix	102-146	45
α-helix	148-150	3
α-helix	154-179	26
α-helix	185-216	32
α-helix	223-247	25

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	611-627	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A	protein	266	Gallus gallus	P12003 (AlphaFold model)
Invasin ipaA	B	protein	21	Shigella flexneri	P18010 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2GDC_1 Vinculin (chains A)
MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVSAVQAAVSNLVRVGKE
TVQTTEDQILKRDMPPAFIKVENACTKLVRAAQMLQADPYSVPARDYLIDGSRGILSGTS
DLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQ
ELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNTKSQGIEEALKNRNFTVEKMSAE
INEIIRVLQLTSWDEDAWASKDTEAM

Sequence of entity 2 (B), FASTA

>2GDC_2 Invasin ipaA (chains B)
XXIYXXAKXVXXXLSKVLXXI

Primary citation

Structural mimicry for vinculin activation by IpaA, a virulence factor of Shigella flexneri. Hamiaux, C., van Eerde, A., Parsot, C. et al. EMBO Rep (2006) 7:794-799. DOI 10.1038/sj.embor.7400753 · 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
3ZDL 2.3 Å, Vinculin head (1-258) in complex with a RIAM fragment
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)
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

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