9DUV: Actin, alpha skeletal muscle

Cryo-EM structure of recombinant R254H ACTA1 phalloidin-stabilized F-actin. Determined by electron microscopy at 3.3 Å resolution. Released 23 Oct 2024.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Homo sapiens, Amanita phalloides
Chains: 13
Atoms: 17,947
Mol. weight: 259.51 kDa
Ligands: MG, ADP
Released: 23 Oct 2024

Explore 9DUV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DUV contains 125 α-helices and 132 β-strands across 9 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-36	2	2
β-strand	38	1	3
β-strand	53-54	2	2
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	3
β-strand	68	1	2
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
β-strand	176-178	3	5
α-helix	182-193	12
α-helix	194-196	3
β-strand	198	1	6
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	7
α-helix	246	1
β-strand	247-250	4	7
α-helix	258-260	3
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	5
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-347	10
α-helix	352-354	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-372	4

Chain B: 19 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	8
β-strand	16-21	6	8
β-strand	29-32	4	8
β-strand	35-36	2	9
β-strand	38	1	10
β-strand	53-54	2	9
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	10
β-strand	68	1	9
β-strand	71-72	2	11
β-strand	75-76	2	11
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	8
α-helix	113-125	13
β-strand	131-136	6	8
α-helix	137-145	9
β-strand	150-155	6	12
β-strand	160-166	7	12
β-strand	169-170	2	12
β-strand	176-178	3	12
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	13
β-strand	247-250	4	13
α-helix	258-260	3
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	12
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	12
α-helix	338-347	10
α-helix	352-354	3
β-strand	357-358	2	8
α-helix	359-365	7
α-helix	369-372	4

Chain C: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	14
β-strand	16-21	6	14
β-strand	29-32	4	14
β-strand	35-36	2	15
β-strand	38	1	16
β-strand	53-54	2	15
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	16
β-strand	68	1	15
β-strand	71-72	2	17
β-strand	75-76	2	17
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	14
α-helix	113-125	13
β-strand	131-136	6	14
α-helix	137-145	9
β-strand	150-155	6	18
β-strand	160-166	7	18
β-strand	169-170	2	18
β-strand	176-178	3	18
α-helix	182-196	15
β-strand	198	1	19
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	20
β-strand	247-250	4	20
α-helix	252-254	3
α-helix	258-260	3
α-helix	264-267	4
α-helix	274-284	11
α-helix	290-295	6
β-strand	297-300	4	18
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	18
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	14
α-helix	359-365	7
α-helix	369-372	4

Chain D: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	21
β-strand	16-21	6	21
β-strand	29-32	4	21
β-strand	35-36	2	22
β-strand	38	1	23
β-strand	53-54	2	22
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	23
β-strand	68	1	22
β-strand	71	1	24
β-strand	76	1	24
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	21
α-helix	113-125	13
β-strand	131-136	6	21
α-helix	137-145	9
β-strand	150-155	6	25
β-strand	160-166	7	25
β-strand	169-170	2	25
β-strand	176-178	3	25
α-helix	182-193	12
α-helix	194-196	3
β-strand	198	1	26
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	27
β-strand	247-250	4	27
α-helix	252-254	3
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-293	4
α-helix	294-296	3
β-strand	297-300	4	25
α-helix	309-320	12
β-strand	329-330	2	25
α-helix	335-337	3
α-helix	338-347	10
α-helix	352-354	3
β-strand	357-358	2	21
α-helix	359-365	7
α-helix	369-372	4

Chain E: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	28
β-strand	16-21	6	28
β-strand	29-32	4	28
β-strand	35-36	2	29
β-strand	38	1	30
β-strand	53-54	2	29
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	30
β-strand	68	1	29
β-strand	71-72	2	31
β-strand	75-76	2	31
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	28
α-helix	113-125	13
β-strand	131-136	6	28
α-helix	137-145	9
β-strand	150-155	6	32
β-strand	160-166	7	32
β-strand	169-170	2	32
β-strand	176-178	3	32
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	33
β-strand	247-250	4	33
α-helix	258-260	3
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-301	5	32
α-helix	309-320	12
β-strand	329-330	2	32
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	28
α-helix	359-365	7
α-helix	369-372	4

Chain F: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	34
β-strand	16-21	6	34
β-strand	29-32	4	34
β-strand	35-36	2	35
β-strand	38	1	36
β-strand	53-54	2	35
α-helix	56-60	5
α-helix	62-64	3
β-strand	65	1	36
β-strand	68	1	35
β-strand	71-72	2	37
β-strand	75-76	2	37
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	34
α-helix	113-125	13
β-strand	131-136	6	34
α-helix	137-145	9
β-strand	150-155	6	38
β-strand	160-166	7	38
β-strand	169-170	2	38
β-strand	176-178	3	38
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	39
β-strand	247-250	4	39
α-helix	253-256	4
α-helix	258-260	3
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	38
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	38
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	34
α-helix	359-363	5
α-helix	369-372	4

Chains N, P and Q: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E, F	protein	375	Homo sapiens	P68133 (AlphaFold model)
phalloidin	M, N, O, P, Q, R, S	protein	7	Amanita phalloides

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

>9DUV_1 Actin, alpha skeletal muscle (chains A, B, C, D, E, F)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNEHFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (M, N, O, P, Q, R, S), FASTA

>9DUV_2 phalloidin (chains M, N, O, P, Q, R, S)
WXATCPA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility. Garg, A., Jansen, S., Greenberg, L. et al. Proc Natl Acad Sci U S A (2024) 121:e2405020121-e2405020121. DOI 10.1073/pnas.2405020121 · PubMed

Other PDB entries of the same protein (UniProt P68133 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RNS 1.14 Å, nSH2 domain of p85-alpha subunit of phosphatidylinositol 3-kinase in complex with an…
7RNU 1.45 Å, nSH2 domain of p85-beta subunit of phosphatidylinositol 3-kinase in complex with an…
7RNV 2.15 Å, SH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide…
9DUU 3.4 Å, Cryo-EM structure of recombinant wildtype ACTA1 phalloidin-stabilized F-actin

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