3RF3: Shigella IpaA-VBS3

Shigella IpaA-VBS3 in complex with human vinculin. Determined by X-ray diffraction at 1.61 Å resolution. Released 27 Apr 2011.

Method: X-ray diffraction
Resolution: 1.61 Å
Organisms: Homo sapiens, Shigella flexneri
Chains: 4
Atoms: 5,187
Mol. weight: 64.43 kDa
Ligands: CAC
Released: 27 Apr 2011

Explore 3RF3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3RF3 contains 27 α-helices and 4 β-strands across 4 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	1
α-helix	7-13	7
α-helix	16-26	11
α-helix	35-39	5
α-helix	41-64	24
α-helix	68-97	30
α-helix	102-145	44
α-helix	148-150	3
α-helix	154-179	26
β-strand	182	1	1
α-helix	185-218	34
α-helix	223-248	26
α-helix	256-257	2

Chain B: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	2
α-helix	7-13	7
α-helix	16-28	13
α-helix	35-39	5
α-helix	41-64	24
α-helix	68-73	6
α-helix	75-97	23
α-helix	103-145	43
α-helix	148-150	3
α-helix	154-179	26
β-strand	182	1	2
α-helix	185-218	34
α-helix	223-248	26
α-helix	256-257	2

Chains C and D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	489-491	3
α-helix	492-507	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A, B	protein	258	Homo sapiens	P18206 (AlphaFold model)
Invasin ipaA	C, D	protein	29	Shigella flexneri	P18010 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3RF3_1 Vinculin (chains A, B)
MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKE
TVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTS
DLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQ
ELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAE
INEIIRVLQLTSWDEDAW

Sequence of entity 2 (C, D), FASTA

>3RF3_2 Invasin ipaA (chains C, D)
GSHMTRETIFEASKKVTNSLSNLISLIGT

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	2

Primary citation

Novel vinculin binding site of the IpaA invasin of Shigella. Park, H., Valencia-Gallardo, C., Sharff, A. et al. J Biol Chem (2011) 286:23214-23221. DOI 10.1074/jbc.M110.184283 · 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
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
9QWO 2.54 Å, Vinculin tail bound to paxillin LD2

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