6VAO: Human cofilin-1 decorated actin filament

Human cofilin-1 decorated actin filament. Determined by electron microscopy at 3.4 Å resolution. Released 8 Jan 2020.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 10
Atoms: 20,480
Mol. weight: 305.4 kDa
Ligands: ADP, MG
Released: 8 Jan 2020

Explore 6VAO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VAO contains 145 α-helices and 173 β-strands across 10 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.

Chains A, B, D and E: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	11
β-strand	16-21	6	11
β-strand	29-32	4	11
β-strand	35-36	2	12
β-strand	37-38	2	13
β-strand	53-54	2	12
α-helix	56-60	5
β-strand	65-66	2	13
α-helix	79-88	10
α-helix	89-93	5
β-strand	96	1	14
α-helix	98-100	3
β-strand	103-107	5	11
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	11
α-helix	137-143	7
β-strand	150-155	6	15
β-strand	160-166	7	15
β-strand	169-170	2	15
β-strand	176-178	3	15
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	16
β-strand	247-250	4	16
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	15
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	15
α-helix	338-347	10
β-strand	357-358	2	11
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 22 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	31
β-strand	16-21	6	31
β-strand	29-32	4	31
β-strand	35-36	2	32
β-strand	37-38	2	33
β-strand	53-54	2	32
α-helix	56-60	5
β-strand	65-66	2	33
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	31
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	31
α-helix	137-143	7
β-strand	150-155	6	34
β-strand	160-166	7	34
β-strand	169-170	2	34
β-strand	176-178	3	34
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	35
β-strand	247-250	4	35
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	34
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	34
α-helix	338-347	10
β-strand	357-358	2	31
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chains F, G, I and J: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	17
α-helix	9-19	11
β-strand	21	1	14
α-helix	29-31	3
β-strand	33-36	4	18
β-strand	38	1	18
β-strand	39-40	2	17
β-strand	46-48	3	17
β-strand	54-56	3	18
β-strand	60	1	19
β-strand	64	1	19
α-helix	69-72	4
β-strand	81-87	7	18
β-strand	89-91	3	20
β-strand	95	1	20
β-strand	98-104	7	18
α-helix	111-119	9
α-helix	121-125	5
β-strand	133-137	5	18
α-helix	140-144	5
α-helix	147-153	7
β-strand	158-161	4	20
β-strand	164-165	2	20

Chain H: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	36
α-helix	9-19	11
α-helix	29-31	3
β-strand	33-36	4	37
β-strand	38	1	37
β-strand	39-40	2	36
β-strand	46-48	3	36
β-strand	54-56	3	37
β-strand	60	1	38
β-strand	64	1	38
α-helix	69-72	4
β-strand	81-87	7	37
β-strand	89-91	3	39
β-strand	95	1	39
β-strand	98-104	7	37
α-helix	111-119	9
α-helix	121-125	5
β-strand	133-137	5	37
α-helix	140-144	5
α-helix	147-153	7
β-strand	158-161	4	39
β-strand	164-165	2	39

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	377	Oryctolagus cuniculus	P68135 (AlphaFold model)
Cofilin-1	F, G, H, I, J	protein	166	Homo sapiens	P23528 (AlphaFold model)

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

>6VAO_1 Actin, alpha skeletal muscle (chains A, B, C, D, E)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (F, G, H, I, J), FASTA

>6VAO_2 Cofilin-1 (chains F, G, H, I, J)
MASGVAVSDGVIKVFNDMKVRKSSTPEEVKKRKKAVLFCLSEDKKNIILEEGKEILVGDV
GQTVDDPYATFVKMLPDKDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASS
KDAIKKKLTGIKHELQANCYEEVKDRCTLAEKLGGSAVISLEGKPL

Ligands and cofactors

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

Primary citation

Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments. Huehn, A.R., Bibeau, J.P., Schramm, A.C. et al. Proc Natl Acad Sci U S A (2020) 117:1478-1484. DOI 10.1073/pnas.1915987117 · 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

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