5O2L: Unconventional myosin-VI

Myosin VI motor domain in the Pre-Transition State. Determined by X-ray diffraction at 2.2 Å resolution. Released 23 May 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Sus scrofa
Chains: 1
Atoms: 6,387
Mol. weight: 90.8 kDa
Ligands: BEF, MG, ADP
Released: 23 May 2018

Explore 5O2L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5O2L contains 50 α-helices and 33 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: 50 helices, 33 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	109-114	6
β-strand	120	1	3
β-strand	123	1	3
α-helix	127-141	15
β-strand	145-150	6	2
α-helix	157-172	16
α-helix	177-179	3
α-helix	180-184	5
α-helix	186-193	8
β-strand	194-197	4	4
β-strand	200-204	5	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	257-262	6
α-helix	268-270	3
α-helix	272-275	4
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	313-326	14
α-helix	331-348	18
β-strand	352-354	3	6
β-strand	362-364	3	6
α-helix	366-368	3
α-helix	369-379	11
α-helix	383-391	9
β-strand	392-395	4	7
β-strand	407-410	4	7
α-helix	411-412	2
α-helix	413-441	29
β-strand	450-456	7	2
α-helix	458-460	3
β-strand	466	1	8
α-helix	468-485	18
α-helix	486-490	5
α-helix	491-499	9
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	566-568	3
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	600-602	3
α-helix	603-610	8
α-helix	615-620	6
β-strand	642	1	9
α-helix	643-660	18
β-strand	662-669	8	2
α-helix	682-691	10
α-helix	694-703	10
β-strand	707-710	4	10
α-helix	711-718	8
α-helix	719-721	3
α-helix	724-726	3
α-helix	731-742	12
β-strand	749-751	3	10
β-strand	755-758	4	10
α-helix	759	1
α-helix	763-770	8
α-helix	774-784	11
α-helix	786-788	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Unconventional myosin-VI	A	protein	785	Sus scrofa	Q29122 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5O2L_1 Unconventional myosin-VI (chains A)
KPVWAPHPTDGFQVGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVEDNCS
LMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLGTMP
PHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIDDRIVE
ANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKEERN
YHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYLKAG
SLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSGGCNL
KNKSTQALEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNARDALA
KTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQQFF
NERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQHFT
SAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDALHMS
LESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRSTGAS
FIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKYMPD
KLARLDPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELVKRV
NHWLI

Ligands and cofactors

ID	Name	Formula	Copies
BEF	Beryllium trifluoride ion	Be F3	1
MG	Magnesium ion	Mg	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

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

Primary citation

An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics. Blanc, F., Isabet, T., Benisty, H. et al. Proc Natl Acad Sci U S A (2018) 115:6213-6218. DOI 10.1073/pnas.1711512115 · PubMed

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
4DBP 2.2 Å, Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure
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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