5L0D: Human Metavinculin(residues 959-1130)

Human Metavinculin(residues 959-1130) in complex with PIP2. Determined by X-ray diffraction at 2.75 Å resolution. Released 31 Aug 2016.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,450
Mol. weight: 78.42 kDa
Ligands: PIO
Released: 31 Aug 2016

Explore 5L0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5L0D contains 24 α-helices and 6 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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	964-979	16
β-strand	980	1	1
α-helix	986-1006	21
α-helix	1012-1037	26
α-helix	1043-1053	11
α-helix	1056-1073	18
α-helix	1081-1118	38
β-strand	1128	1	1

Chain B: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	964-977	14
β-strand	980	1	2
α-helix	986-1006	21
α-helix	1012-1038	27
α-helix	1043-1053	11
α-helix	1056-1073	18
α-helix	1081-1115	35
β-strand	1128	1	2

Chain C: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	964-977	14
β-strand	980	1	3
α-helix	986-1006	21
α-helix	1011-1038	28
α-helix	1043-1053	11
α-helix	1056-1075	20
α-helix	1081-1114	34
β-strand	1128	1	3

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	964-977	14
α-helix	986-1006	21
α-helix	1011-1038	28
α-helix	1043-1073	31
α-helix	1081-1113	33
α-helix	1119-1121	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vinculin	A, B, C, D	protein	172	Homo sapiens	P18206 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5L0D_1 Vinculin (chains A, B, C, D)
NQPVNQPILAAAQSLHREATKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQC
AKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTN
ISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKT

Ligands and cofactors

ID	Name	Formula	Copies
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	3

Primary citation

Differential lipid binding of vinculin isoforms promotes quasi-equivalent dimerization. Chinthalapudi, K., Rangarajan, E.S., Brown, D.T. et al. Proc Natl Acad Sci U S A (2016) 113:9539-9544. DOI 10.1073/pnas.1600702113 · 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

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