8R9V: Primed actomyosin-5a complex

CryoEM structure of the primed actomyosin-5a complex. Determined by electron microscopy at 4.4 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 4.4 Å
Organisms: Mus musculus, Oryctolagus cuniculus
Chains: 4
Atoms: 14,851
Mol. weight: 219.81 kDa
Ligands: PO4, ADP, MG
Released: 11 Dec 2024

Explore 8R9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R9V contains 96 α-helices and 91 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: 39 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	12-17	6	1
β-strand	21-27	7	1
α-helix	30-32	3
β-strand	37-42	6	1
β-strand	47-51	5	1
β-strand	53	1	2
β-strand	58	1	2
α-helix	59-60	2
β-strand	61-62	2	1
α-helix	63-65	3
β-strand	73	1	3
α-helix	74-76	3
α-helix	82-91	10
α-helix	92-96	5
β-strand	100-103	4	3
β-strand	106-110	5	3
α-helix	121-127	7
α-helix	139-153	15
β-strand	157-162	6	3
β-strand	164	1	4
α-helix	169-183	15
α-helix	184-186	3
α-helix	190-205	16
β-strand	208-209	2	5
β-strand	217-218	2	5
β-strand	220-228	9	3
β-strand	234-244	11	3
α-helix	247-250	4
β-strand	259	1	5
α-helix	260-268	9
α-helix	272-275	4
α-helix	286-289	4
α-helix	301-314	14
α-helix	319-335	17
β-strand	341-343	3	6
β-strand	347-349	3	6
α-helix	355-364	10
α-helix	368-376	9
β-strand	377-379	3	7
β-strand	388-390	3	7
α-helix	393-422	30
β-strand	431-437	7	3
β-strand	441	1	4
α-helix	449-465	17
α-helix	466-471	6
α-helix	472-479	8
α-helix	486-488	3
α-helix	494-500	7
α-helix	505-514	10
α-helix	520-531	12
β-strand	538-539	2	8
β-strand	547-551	5	8
β-strand	556-560	5	8
α-helix	565-569	5
α-helix	574-581	8
α-helix	587-592	6
α-helix	635-651	17
β-strand	654-661	8	3
α-helix	674-684	11
α-helix	686-695	10
β-strand	699-702	4	9
α-helix	703-709	7
α-helix	711-713	3
α-helix	723-734	12
α-helix	738-740	3
β-strand	741-743	3	9
β-strand	747-750	4	9
α-helix	754-773	20

Chain B: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	9-12	4	10
β-strand	17-22	6	10
β-strand	30-33	4	10
β-strand	36-39	4	11
β-strand	54-55	2	11
α-helix	57-60	4
β-strand	63	1	11
β-strand	66-69	4	11
β-strand	72-73	2	12
β-strand	76-77	2	12
α-helix	80-89	10
α-helix	90-94	5
α-helix	99-101	3
β-strand	104-108	5	10
α-helix	114-128	15
β-strand	132-137	6	10
α-helix	138-146	9
β-strand	151-156	6	13
β-strand	161-167	7	13
β-strand	170-171	2	13
β-strand	177-179	3	13
α-helix	183-197	15
α-helix	204-217	14
α-helix	224-234	11
β-strand	239-242	4	14
β-strand	248-251	4	14
α-helix	254-260	7
α-helix	265-267	3
α-helix	272-274	3
α-helix	275-285	11
α-helix	288-295	8
β-strand	298-301	4	13
α-helix	303-305	3
α-helix	310-321	12
β-strand	330-331	2	13
α-helix	340-348	9
β-strand	358-359	2	10
α-helix	360-366	7
α-helix	368-370	3
α-helix	371-374	4

Chain C: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	15
β-strand	16-21	6	15
β-strand	29-32	4	15
β-strand	35-38	4	16
β-strand	53-54	2	16
α-helix	56-59	4
β-strand	62	1	16
β-strand	65-68	4	16
β-strand	71-72	2	17
β-strand	75-76	2	17
α-helix	79-87	9
α-helix	88-93	6
β-strand	103-107	5	15
α-helix	113-125	13
β-strand	131-136	6	15
α-helix	137-144	8
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	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	19
β-strand	247-250	4	19
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	18
α-helix	309-320	12
β-strand	329-330	2	18
α-helix	339-348	10
α-helix	350-352	3
β-strand	357-358	2	15
α-helix	359-365	7
α-helix	369-374	6

Chain D: 19 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	20
β-strand	16-21	6	20
β-strand	29-32	4	20
α-helix	34	1
β-strand	35-38	4	21
β-strand	41	1	13
β-strand	53-54	2	21
α-helix	56-59	4
β-strand	62	1	21
β-strand	65-68	4	21
β-strand	71-72	2	22
β-strand	75-76	2	22
α-helix	79-87	9
α-helix	88-93	6
β-strand	103-107	5	20
α-helix	113-126	14
β-strand	131-136	6	20
α-helix	137-145	9
β-strand	150-155	6	23
β-strand	160-166	7	23
β-strand	169-170	2	23
β-strand	176-178	3	23
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	24
β-strand	247-250	4	24
α-helix	253-259	7
α-helix	264-266	3
α-helix	274-284	11
α-helix	287-294	8
β-strand	297-300	4	23
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	23
α-helix	338-348	11
β-strand	357-358	2	20
α-helix	359-365	7
α-helix	369-374	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Unconventional myosin-Va	A	protein	801	Mus musculus	Q99104 (AlphaFold model)
Actin, alpha skeletal muscle	B, C, D	protein	376	Oryctolagus cuniculus	P68135 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8R9V_1 Unconventional myosin-Va (chains A)
MAASELYTKFARVWIPDPEEVWKSAELLKDYKPGDKVLLLHLEEGKDLEYRLDPKTGELP
HLRNPDILVGENDLTALSYLHEPAVLHNLRVRFIDSKLIYTYCGIVLVAINPYEQLPIYG
EDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYF
ATVSGSASEANVEEKVLASNPIMESIGNAKTTRNDNASRFGKYIEIGFDKRYRIIGANMR
TYLLEKSRVVFQAEEERNYHIFYQLCASAKLPEFKMLRLGNADSFHYTKQGGSPMIEGVD
DAKEMAHTRQACTLLGISESYQMGIFRILAGILHLGNVGFASRDSDSCTIPPKHEPLTIF
CDLMGVDYEEMCHWLCHRKLATATETYIKPISKLQATNARDALAKHIYAKLFNWIVDHVN
QALHSAVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKE
QIPWTLIDFYDNQPCINLIESKLGILDLLDEECKMPKGTDDTWAQKLYNTHLNKCALFEK
PRMSNKAFIIKHFADKVEYQCEGFLEKNKDTVFEEQIKVLKSSKFKMLPELFQAISPTSA
TSSGRTPLTRVPVKPTKGRPGQTAKEHKKTVGHQFRNSLHLLMETLNATTPHYVRCIKPN
DFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDVLGDRK
QTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKLRADKLRAACIRIQKTIRGWLLRK
RYLCMQRAAITVQDYKDDDDK

Sequence of entity 2 (B, C, D), FASTA

>8R9V_2 Actin, alpha skeletal muscle (chains B, C, D)
XDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKM
TQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLD
LAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKS
YELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVM
SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITK
QEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
MG	Magnesium ion	Mg	4

Primary citation

Swinging lever mechanism of myosin directly shown by time-resolved cryo-EM. Klebl, D.P., McMillan, S.N., Risi, C. et al. Nature (2025) 642:519-526. DOI 10.1038/s41586-025-08876-5 · PubMed

Other PDB entries of the same protein (UniProt Q99104 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6KU0 1.6 Å, Crystal structure of MyoVa-GTD in complex with MICAL1-GTBM
4KP3 2.4 Å, Crystal Structure of MyoVa-GTD in Complex with Two Cargos
3WB8 2.5 Å, Crystal Structure of MyoVa-GTD
2IX7 2.5 Å, Structure of apo-calmodulin bound to unconventional myosin V
4ZLK 2.5 Å, Crystal structure of mouse myosin-5a in complex with calcium-bound calmodulin
8RBF 4.2 Å, CryoEM structure of the post-powerstroke actomyosin-5a complex
7YV9 4.78 Å, Cryo-EM structure of full-length Myosin Va in the autoinhibited state
8RBG 4.9 Å, CryoEM structure of primed myosin-5a (ADP-Pi state)
8OF8 7.5 Å, Cryo-EM structure of actomyosin-5a-S1 with the full-length lever (nucleotide free)

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