8W41: Myosin VI in the autoinhibited state

Cryo-EM structure of Myosin VI in the autoinhibited state. Determined by electron microscopy at 3.54 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Mus musculus, Homo sapiens
Chains: 3
Atoms: 11,859
Mol. weight: 183.36 kDa
Ligands: PO4, MG, ADP, CA
Released: 21 Feb 2024

Explore 8W41 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W41 contains 70 α-helices and 42 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: 52 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	5
β-strand	16-21	6	5
β-strand	28-33	6	5
β-strand	41-44	4	5
α-helix	45-47	3
β-strand	49-50	2	5
β-strand	61	1	6
α-helix	62-64	3
α-helix	70-82	13
β-strand	87-90	4	6
β-strand	93-97	5	6
α-helix	109-115	7
α-helix	118-119	2
α-helix	127-140	14
β-strand	145-150	6	6
α-helix	157-170	14
α-helix	178-184	7
α-helix	186-193	8
β-strand	194-195	2	7
β-strand	203-204	2	7
β-strand	207-214	8	6
β-strand	220	1	6
β-strand	224-228	5	6
α-helix	247-254	8
α-helix	257-263	7
α-helix	268-270	3
α-helix	272-275	4
β-strand	282	1	8
α-helix	285-290	6
α-helix	298-303	6
β-strand	306	1	8
α-helix	313-326	14
α-helix	331-349	19
β-strand	352-354	3	9
β-strand	362-364	3	9
α-helix	367-378	12
α-helix	383-391	9
β-strand	392	1	10
β-strand	410	1	10
α-helix	413-442	30
β-strand	450-456	7	6
β-strand	466	1	11
α-helix	468-485	18
α-helix	486-490	5
α-helix	491-499	9
α-helix	512-519	8
α-helix	525-533	9
α-helix	540-550	11
β-strand	557-558	2	11
α-helix	560-562	3
α-helix	568-570	3
α-helix	573-575	3
β-strand	576-580	5	11
β-strand	585-589	5	11
α-helix	593-596	4
β-strand	598	1	12
α-helix	603-610	8
α-helix	615-621	7
β-strand	642	1	12
α-helix	643-660	18
β-strand	662-669	8	6
α-helix	682-691	10
α-helix	694-701	8
β-strand	707-710	4	13
α-helix	711-719	9
α-helix	724-727	4
α-helix	731-741	11
β-strand	755-758	4	13
α-helix	763-769	7
α-helix	774-828	55
α-helix	834-859	26
α-helix	864-887	24
α-helix	892-919	28
α-helix	923-978	56
α-helix	983-1020	38
α-helix	1082-1087	6
α-helix	1097-1118	22
α-helix	1132-1135	4
β-strand	1168-1174	7	14
α-helix	1178-1180	3
β-strand	1192-1198	7	14
β-strand	1201-1208	8	14
α-helix	1231-1234	4
β-strand	1244	1	14
α-helix	1246-1254	9
α-helix	1258-1267	10

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	1
α-helix	30-39	10
α-helix	46-55	10
β-strand	64	1	1
α-helix	66-73	8
α-helix	79-93	15
β-strand	101	1	2
α-helix	103-113	11
α-helix	119-129	11
β-strand	137	1	2
α-helix	139-147	9

Chain I: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	29	1	3
α-helix	30-37	8
α-helix	46-56	11
α-helix	57-59	3
β-strand	63	1	3
α-helix	66-78	13
α-helix	83-92	10
β-strand	100-101	2	4
α-helix	103-112	10
α-helix	119-123	5
α-helix	124-128	5
β-strand	137-138	2	4
α-helix	139-147	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calmodulin-1	B, I	protein	149	Mus musculus	P0DP26 (AlphaFold model)
Unconventional myosin-VI	A	protein	1285	Homo sapiens	Q9UM54 (AlphaFold model)

Sequence of entity 1 (B, I), FASTA

>8W41_1 Calmodulin-1 (chains B, I)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Sequence of entity 2 (A), FASTA

>8W41_2 Unconventional myosin-VI (chains A)
MEDGKPVWAPHPTDGFQMGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVE
DNCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSEAIKSYQGKSL
GTRPPHVFAIADKAFRDMKVLKMSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIDD
RIVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGK
EERNYHIFYRLCAGASEDIREKLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEY
LKAGSMKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSG
GCNLKNKSAQSLEYCAELLGLDQDDLRVSLTTRVMLTTAGGTKGTVIKVPLKVEQANNAR
DALAKTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKL
QQFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEAKLVGILDILDEENRLPQPSD
QHFTSAVHQKHKDHFRLTIPRKSKLAVHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDA
LHMSLESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRS
TGASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGYPSRASFHELYNMYKK
YMPDKLARLDPRLFCKALFKALGLNENDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAEL
VKRVNHWLTCSRWKKVQWCSLSVIKLKNKIKYRAEACIKMQKTIRMWLCKRRHKPRIDGL
VKVGTLKKRLDKFNEVVSVLKDGKPEMNKQIKNLEISIDTLMAKIKSTMMTQEQIQKEYD
ALVKSSEELLSALQKKKQQEEEAERLRRIQEEMEKERKRREEDEKRRRKEEEERRMKLEM
EAKRKQEEEERKKREDDEKRIQAEVEAQLARQKEEESQQQAVLEQERRDRELALRIAQSE
AELISDEAQADLALRRNDGTRPKMTPEQMAKEMSEFLSRGPAVLATKAAAGTKKYDLSKW
KYAELRDTINTSCDIELLAACREEFHRRLKVYHAWKSKNKKRNTETEQRAPKSVTDYDFA
PFLNNSPQQNPAAQIPARQREIEMNRQQRFFRIPFIRPADQYKDPQSKKKGWWYAHFDGP
WIARQMELHPDKPPILLVAGKDDMEMCELNLEETGLTRKRGAEILPRQFEEIWERCGGIQ
YLQNAIESRQARPTYATAMLQSLLK

Ligands and cofactors

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

Primary citation

Autoinhibition and activation of myosin VI revealed by its cryo-EM structure. Niu, F., Li, L., Wang, L. et al. Nat Commun (2024) 15:1187-1187. DOI 10.1038/s41467-024-45424-7 · PubMed

Other PDB entries of the same protein (UniProt P0DP26 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7CQP 1.9 Å, Complex of TRPC4 and Calmodulin_Nlobe
3WFN 1.95 Å, Crystal Structure of Nav1.6 IQ motif in complex with apo-CaM
4HEX 2.0 Å, A novel conformation of calmodulin
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
4E53 2.69 Å, Calmodulin and Nm peptide complex
4E50 2.7 Å, Calmodulin and Ng peptide complex
9CFV 2.7 Å, Cryo-EM structure of delta-NTR myosin-1c bound to F-actin
9CFX 2.7 Å, Cryo-EM structure of myosin-1c bound to F-actin in the Rigor state
9CFU 2.8 Å, Cryo-EM structure of myosin-1c bound to F-actin in the ADP-A state
9CFW 3.0 Å, Cryo-EM structure of myosin-1c bound to F-actin in the ADP-B state
8PB1 3.5 Å, Cryo-EM structure of a pre-dimerized murine IL-12 complete extracellular signaling…

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