3JBI: MDFF model of the vinculin tail domain

MDFF model of the vinculin tail domain bound to F-actin. Determined by electron microscopy at 8.5 Å resolution. Released 4 Nov 2015.

Method: Electron microscopy
Resolution: 8.5 Å
Organisms: Oryctolagus cuniculus, Gallus gallus
Chains: 3
Atoms: 6,777
Mol. weight: 112.87 kDa
Ligands: MG, ADP
Released: 4 Nov 2015

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

Secondary structure: helices and β-sheets

3JBI contains 47 α-helices and 39 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: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
β-strand	17-21	5	1
β-strand	29-31	3	1
β-strand	35-37	3	2
α-helix	41	1
β-strand	42	1	3
β-strand	53-54	2	2
α-helix	57-60	4
β-strand	66-68	3	2
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
β-strand	103-107	5	1
α-helix	115-127	13
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	150-156	7	5
β-strand	159-166	8	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	183-194	12
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	252-259	8
α-helix	264-266	3
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	311-320	10
α-helix	322	1
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-355	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-370	5

Chain B: 19 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	7
β-strand	17-21	5	7
β-strand	29-31	3	7
β-strand	35-38	4	8
β-strand	53-54	2	8
α-helix	57-60	4
β-strand	65-68	4	8
β-strand	71-72	2	9
β-strand	75-76	2	9
α-helix	79-87	9
α-helix	88-94	7
β-strand	103-107	5	7
α-helix	115-127	13
β-strand	131-132	2	10
β-strand	134-136	3	7
α-helix	137-143	7
β-strand	149-156	8	3
β-strand	159-166	8	3
β-strand	169-170	2	3
α-helix	172-174	3
β-strand	176-178	3	3
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	252-259	8
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-300	4	3
α-helix	302-304	3
α-helix	311-320	10
α-helix	322	1
α-helix	335-348	14
α-helix	352-355	4
β-strand	357-358	2	10
α-helix	359-365	7

Chain V: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	918-938	21
α-helix	941-943	3
α-helix	944-971	28
α-helix	975-985	11
α-helix	987-1005	19
α-helix	1013-1044	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Vinculin	V	protein	254	Gallus gallus	P12003 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3JBI_1 Actin, alpha skeletal muscle (chains A, B)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (V), FASTA

>3JBI_2 Vinculin (chains V)
GSEEKDEEFPEQKAGEAINQPMMMAARQLHDEARKWSSKPVTVINEAAEAGVDIDEEDDA
DVEFSLPSDIEDDYEPELLLMPTNQPVNQPILAAAQSLHREATKWSSKGNDIIAAAKRMA
LLMAEMSRLVRGGSGNKRALIQCAKDIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCER
IPTISTQLKILSTVKATMLGRTNISDEESEQATEMLVHNAQNLMQSVKETVREAEAASIK
IRTDAGFTLRWVRK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

The Structural Basis of Actin Organization by Vinculin and Metavinculin. Kim, L.Y., Thompson, P.M., Lee, H.T. et al. J Mol Biol (2016) 428:10-25. DOI 10.1016/j.jmb.2015.09.031 · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

Browse structure collections

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