4DBP: Myosin-VI

Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure. Determined by X-ray diffraction at 2.2 Å resolution. Released 30 Jan 2013.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Sus scrofa, Drosophila melanogaster
Chains: 2
Atoms: 8,335
Mol. weight: 111.39 kDa
Ligands: CA, IPA, TBU
Released: 30 Jan 2013

Explore 4DBP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DBP contains 55 α-helices and 32 β-strands across 2 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: 47 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	15-24	10	1
β-strand	28-33	6	1
β-strand	41-44	4	1
α-helix	45-47	3
β-strand	49-50	2	1
β-strand	61	1	2
α-helix	62-64	3
α-helix	70-82	13
β-strand	87-90	4	2
β-strand	93-97	5	2
α-helix	104-107	4
α-helix	109-115	7
α-helix	118-119	2
α-helix	127-141	15
β-strand	145-150	6	2
α-helix	157-172	16
α-helix	176-184	9
α-helix	186-193	8
β-strand	194-195	2	3
β-strand	203-204	2	3
β-strand	207-214	8	2
β-strand	220-228	9	2
α-helix	233-235	3
β-strand	245	1	3
α-helix	246-254	9
α-helix	257-263	7
α-helix	268-270	3
α-helix	272-275	4
α-helix	280-281	2
β-strand	282	1	4
α-helix	285-290	6
α-helix	293-295	3
α-helix	298-303	6
β-strand	306	1	4
α-helix	313-326	14
α-helix	331-347	17
β-strand	352-354	3	5
β-strand	362-364	3	5
α-helix	366-368	3
α-helix	369-378	10
α-helix	383-391	9
β-strand	392-396	5	6
β-strand	406-410	5	6
α-helix	411-412	2
α-helix	413-440	28
β-strand	450-456	7	2
α-helix	468-498	31
α-helix	505-507	3
α-helix	512-519	8
α-helix	525-532	8
α-helix	540-550	11
β-strand	557-558	2	7
α-helix	560-562	3
α-helix	566-568	3
α-helix	573-575	3
β-strand	576-581	6	7
β-strand	584-589	6	7
α-helix	593-596	4
α-helix	603-610	8
α-helix	615-621	7
α-helix	643-659	17
β-strand	662-669	8	2
α-helix	682-691	10
α-helix	694-701	8
β-strand	707-710	4	8
α-helix	711-718	8
α-helix	719-721	3
α-helix	724-727	4
α-helix	731-742	12
β-strand	749-751	3	8
β-strand	755-758	4	8
α-helix	762-772	11
α-helix	774-783	10
α-helix	785-813	29

Chain C: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	27	1	9
α-helix	29-38	10
α-helix	45-55	11
β-strand	63	1	9
α-helix	65-71	7
α-helix	81-92	12
β-strand	100	1	10
α-helix	102-112	11
α-helix	118-128	11
β-strand	136	1	10
α-helix	138-145	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myosin-VI	A	protein	814	Sus scrofa	Q29122 (AlphaFold model)
Calmodulin	C	protein	149	Drosophila melanogaster	P62152 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DBP_1 Myosin-VI (chains A)
EDGKPVWAPHPTDGFQVGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVED
NCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLG
TMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIYDR
IVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKE
ERNYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYL
KAGSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSGG
CNLKNKSTQALEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNARD
ALAKTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQ
QFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQ
HFTSAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDAL
HMSLESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRST
GASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKY
MPDKLARLDPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELV
KRVNHWLICSRWKKVQWCSLSVIKLKNKIKYRAE

Sequence of entity 2 (C), FASTA

>4DBP_2 Calmodulin (chains C)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVTMMTSK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
IPA	Isopropyl alcohol	C3 H8 O	1
TBU	Tertiary-butyl alcohol	C4 H10 O	2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Mutations in myosin VI that cause a loss of coordination between heads provide insights into the structural changes underlying force generation and the importance of gating. Song, L., Pylypenko, O., Yang, Z. et al. To be published.

Other PDB entries of the same protein (UniProt Q29122 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V26 1.75 Å, Myosin VI (MD) pre-powerstroke state (Mg.ADP.VO4)
4DBR 1.95 Å, Myosin VI D179Y (MD) pre-powerstroke state
2X51 2.2 Å, M6 delta Insert1
3L9I 2.2 Å, Myosin VI nucleotide-free (mdinsert2) L310G mutant crystal structure
5O2L 2.2 Å, Myosin VI motor domain in the Pre-Transition State
2VB6 2.3 Å, Myosin VI (MD-insert2-CaM, Delta Insert1) Post-rigor state (crystal form 2)
2BKH 2.4 Å, Myosin VI nucleotide-free (MDInsert2) crystal structure
2VAS 2.4 Å, Myosin VI (MD-insert2-CaM, Delta-Insert1) Post-rigor state
4ANJ 2.6 Å, MYOSIN VI (MDinsert2-GFP fusion) PRE-POWERSTROKE STATE (MG.ADP.AlF4)
4DBQ 2.6 Å, MYOSIN VI D179Y (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state
3GN4 2.7 Å, Myosin lever arm
2BKI 2.9 Å, Myosin VI nucleotide-free (MDinsert2-IQ) crystal structure

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