7PMD: Unconventional myosin-Va

Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state (AppNHp, central 1er). Determined by electron microscopy at 2.9 Å resolution. Released 22 Dec 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Gallus gallus, Oryctolagus cuniculus, Amanita phalloides
Chains: 4
Atoms: 10,189
Mol. weight: 152.38 kDa
Ligands: ANP, MG, ADP
Released: 22 Dec 2021

Explore 7PMD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PMD contains 72 α-helices and 51 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: 37 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	1
β-strand	22-27	6	1
β-strand	37-41	5	1
β-strand	47-51	5	1
α-helix	59-61	3
β-strand	62	1	1
β-strand	73	1	2
α-helix	74-76	3
α-helix	82-91	10
α-helix	92-96	5
β-strand	100-103	4	2
β-strand	106-110	5	2
α-helix	117-119	3
α-helix	121-127	7
α-helix	139-152	14
β-strand	157-162	6	2
α-helix	169-184	16
α-helix	192-207	16
β-strand	208-211	4	3
β-strand	214-218	5	3
β-strand	221-228	8	2
β-strand	234-242	9	2
α-helix	246-249	4
α-helix	260-268	9
α-helix	273-277	5
α-helix	286-289	4
α-helix	301-314	14
α-helix	319-336	18
β-strand	341-344	4	4
β-strand	347-349	3	4
α-helix	350-351	2
α-helix	355-364	10
α-helix	368-374	7
β-strand	377-382	6	5
β-strand	385-390	6	5
α-helix	393-423	31
α-helix	428-429	2
β-strand	431-438	8	2
α-helix	449-479	31
α-helix	484-486	3
α-helix	493-500	8
α-helix	505-514	10
α-helix	520-531	12
β-strand	538-539	2	6
β-strand	547-551	5	6
β-strand	556-560	5	6
α-helix	564-568	5
α-helix	574-581	8
α-helix	588-593	6
α-helix	631-633	3
α-helix	636-652	17
β-strand	655	1	2
β-strand	658-662	5	2
α-helix	675-684	10
α-helix	687-695	9
β-strand	700-703	4	7
α-helix	704-711	8
α-helix	712-714	3
α-helix	724-735	12
α-helix	739-741	3
β-strand	742-744	3	7
β-strand	748-751	4	7
α-helix	753-791	39

Chain B: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
β-strand	26-28	3	13
α-helix	29-38	10
α-helix	45-52	8
α-helix	57-62	6
β-strand	64-66	3	13
α-helix	67-78	12
α-helix	87-94	8
β-strand	105	1	14
α-helix	106-115	10
α-helix	119-121	3
α-helix	122-129	8
β-strand	133	1	15
β-strand	138	1	14
β-strand	139	1	15
α-helix	141-149	9

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	8
β-strand	16-21	6	8
β-strand	29-32	4	8
β-strand	35-38	4	9
α-helix	41-42	2
β-strand	53-54	2	9
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	9
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
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	11
β-strand	160-166	7	11
β-strand	169-170	2	11
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	184-195	12
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-256	4
α-helix	258-261	4
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	11
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	11
α-helix	335-337	3
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	8
α-helix	359-365	7
α-helix	369-373	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Unconventional myosin-Va	A	protein	792	Gallus gallus	Q02440 (AlphaFold model)
Actin, alpha skeletal muscle	C	protein	377	Oryctolagus cuniculus	P68135 (AlphaFold model)
Phalloidin	H	protein	7	Amanita phalloides
Myosin light chain 6B	B	protein	151	Homo sapiens	P14649 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7PMD_1 Unconventional myosin-Va (chains A)
MAASELYTKYARVWIPDPEEVWKSAELLKDYKPGDKVLQLRLEEGKDLEYCLDPKTKELP
PLRNPDILVGENDLTALSYLHEPAVLHNLKVRFIDSKLIYTYCGIVLVAINPYEQLPIYG
EDIINAYSGQNMGDMDPHIFAVAEEAYKQMARDERNQSIIVSGESGAGKTVSAKYAMRYF
ATVSGSASEANVEEKVLASNPIMESIGNAKTTRNDNSSRFGKYIEIGFDKRYRIIGANMR
TYLLEKSRVVFQAEEERNYHIFYQLCASAALPEFKTLRLGNANYFHYTKQGGSPVIDGID
DAKEMVNTRQACTLLGISDSYQMGIFRILAGILHLGNVEFASRDSDSCAIPPKHDPLTIF
CDLMGVDYEEMAHWLCHRKLATATETYIKPISKLHAINARDALAKHIYANLFNWIVDHVN
KALHSTVKQHSFIGVLDIYGFETFEINSFEQFCINYANEKLQQQFNMHVFKLEQEEYMKE
QIPWTLIDFYDNQPCINLIEAKMGVLDLLDEECKMPKGSDDTWAQKLYNTHLNKCALFEK
PRLSNKAFIIKHFADKVEYQCEGFLEKNKDTVYEEQIKVLKSSKKFKLLPELFQDEEKAI
SPTSATPSGRVPLSRTPVKPAKARPGQTSKEHKKTVGHQFRNSLHLLMETLNATTPHYVR
CIKPNDFKFPFTFDEKRAVQQLRACGVLETIRISAAGFPSRWTYQEFFSRYRVLMKQKDV
LSDRKQTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIRADKLRAACIRIQKTIRG
WLMRKKYMRMRR

Sequence of entity 2 (C), FASTA

>7PMD_2 Actin, alpha skeletal muscle (chains C)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 3 (H), FASTA

>7PMD_3 Phalloidin (chains H)
WXATCPA

Sequence of entity 4 (B), FASTA

>7PMD_4 Myosin light chain 6B (chains B)
MIEFNKDQLEEFKEAFELFDRVGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEL
KSRRVDFETFLPMLQAVAKNRGQGTYEDYLEGFRVFDKEGNGKVMGAELRHVLTTLGEKM
TEEEVETVLAGHEDSNGCINYEAFLKHILSV

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

High-resolution structures of the actomyosin-V complex in three nucleotide states provide insights into the force generation mechanism. Pospich, S., Sweeney, H.L., Houdusse, A. et al. Elife (2021) 10. DOI 10.7554/eLife.73724 · PubMed

Other PDB entries of the same protein (UniProt Q02440 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1W7J 2.0 Å, Crystal Structure Of Myosin V Motor With Essential Light Chain + ADP-BeFx - Near Rigor
1OE9 2.05 Å, Crystal structure of Myosin V motor with essential light chain-nucleotide-free
1W8J 2.7 Å, Crystal Structure Of Myosin V Motor Domain - Nucleotide-Free
7PME 2.9 Å, Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state…
1W7I 3.0 Å, Crystal Structure Of Myosin V Motor Without nucleotide soaked in 10 mM MgADP
7PM6 3.0 Å, Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 3er/2er)
7PM5 3.1 Å, Cryo-EM structure of the actomyosin-V complex in the strong-ADP state (central 1er)
7PLU 3.2 Å, Cryo-EM structure of the actomyosin-V complex in the rigor state (central 3er/2er)
7PLY 3.2 Å, Cryo-EM structure of the actomyosin-V complex in the rigor state (central 1er, young…
7PLZ 3.2 Å, Cryo-EM structure of the actomyosin-V complex in the rigor state (central 3er/2er, young…
7PLT 3.3 Å, Cryo-EM structure of the actomyosin-V complex in the rigor state (central 1er)
7PMG 3.3 Å, Cryo-EM structure of the actomyosin-V complex in the post-rigor transition state…

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