4DJ9: Human vinculin head domain Vh1

Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099). Determined by X-ray diffraction at 2.25 Å resolution. Released 29 Feb 2012.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,103
Mol. weight: 31.81 kDa
Released: 29 Feb 2012

Explore 4DJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DJ9 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	7-29	23
α-helix	37-39	3
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	185-214	30
α-helix	222-248	27

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2079-2098	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A	protein	258	Homo sapiens	P18206 (AlphaFold model)
Talin-1	B	protein	29	Homo sapiens	Q9Y490 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DJ9_1 Vinculin (chains A)
MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKE
TVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTS
DLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQ
ELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAE
INEIIRVLQLTSWDEDAW

Sequence of entity 2 (B), FASTA

>4DJ9_2 Talin-1 (chains B)
ETQVVLINAVKDVAKALGDLISATKAAAG

Primary citation

Crystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin. Yogesha, S.D., Rangarajan, E.S., Vonrhein, C. et al. Protein Sci (2012) 21:583-588. DOI 10.1002/pro.2041 · 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
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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