4DBR: Myosin VI D179Y (MD) pre-powerstroke state

Myosin VI D179Y (MD) pre-powerstroke state. Determined by X-ray diffraction at 1.95 Å resolution. Released 30 Jan 2013.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Sus scrofa
Chains: 1
Atoms: 6,862
Mol. weight: 90.73 kDa
Ligands: VO4, MG, ADP
Released: 30 Jan 2013

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

Secondary structure: helices and β-sheets

4DBR contains 47 α-helices and 32 β-strands across 1 chain. 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, 32 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	15-24	10	1
β-strand	29-33	5	1
β-strand	41-43	3	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	109-115	7
α-helix	118-119	2
α-helix	127-141	15
β-strand	145-150	6	2
β-strand	152	1	3
α-helix	157-172	16
α-helix	177-184	8
α-helix	186-193	8
β-strand	194-195	2	4
β-strand	203-204	2	4
β-strand	207-214	8	2
β-strand	220-228	9	2
α-helix	233-235	3
β-strand	245	1	4
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	5
α-helix	285-290	6
α-helix	293-295	3
α-helix	298-303	6
β-strand	306	1	5
α-helix	313-327	15
α-helix	331-348	18
β-strand	352-354	3	6
β-strand	362-364	3	6
α-helix	366-368	3
α-helix	369-378	10
α-helix	383-391	9
β-strand	392-393	2	7
β-strand	409-410	2	7
α-helix	413-440	28
β-strand	450-456	7	2
α-helix	457-459	3
β-strand	460	1	3
α-helix	468-484	17
α-helix	485-491	7
α-helix	492-498	7
α-helix	503-505	3
α-helix	512-519	8
α-helix	525-533	9
α-helix	540-550	11
β-strand	557-558	2	8
α-helix	560-562	3
α-helix	566-569	4
α-helix	573-575	3
β-strand	576-581	6	8
β-strand	584-589	6	8
α-helix	593-596	4
β-strand	598	1	9
α-helix	603-610	8
α-helix	615-620	6
β-strand	642	1	9
α-helix	643-659	17
β-strand	662-669	8	2
α-helix	682-691	10
α-helix	694-700	7
β-strand	707-710	4	10
α-helix	711-719	9
α-helix	724-728	5
α-helix	731-741	11
α-helix	746-748	3
β-strand	749-751	3	10
β-strand	755-758	4	10
α-helix	763-770	8
α-helix	774-787	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myosin-VI	A	protein	786	Sus scrofa	Q29122 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DBR_1 Myosin-VI (chains A)
AKPVWAPHPTDGFQVGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVEDNC
SLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLGTM
PPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIYDRIV
EANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKEER
NYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYLKA
GSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSGGCN
LKNKSTQALEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNARDAL
AKTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQQF
FNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQHF
TSAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDALHM
SLESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRSTGA
SFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKYMP
DKLARLDPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELVKR
VNHWLI

Ligands and cofactors

ID	Name	Formula	Copies
VO4	Vanadate ion	O4 V	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

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)
2X51 2.2 Å, M6 delta Insert1
3L9I 2.2 Å, Myosin VI nucleotide-free (mdinsert2) L310G mutant crystal structure
4DBP 2.2 Å, Myosin VI nucleotide-free (MDINSERT2) D179Y 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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