4PFP: Unconventional myosin-VI

Myosin VI motor domain in the Pi release state (with Pi) space group P21. Determined by X-ray diffraction at 2.32 Å resolution. Released 29 Apr 2015.

Method: X-ray diffraction
Resolution: 2.32 Å
Organism: Sus scrofa
Chains: 2
Atoms: 12,526
Mol. weight: 180.96 kDa
Ligands: PO4, PGO, ADP, MG
Released: 29 Apr 2015

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

Secondary structure: helices and β-sheets

4PFP contains 92 α-helices and 60 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: 46 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	1
β-strand	15-25	11	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	109-115	7
α-helix	118-119	2
α-helix	127-141	15
β-strand	145-150	6	2
α-helix	157-172	16
α-helix	177-184	8
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	257-262	6
α-helix	268-270	3
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	313-327	15
α-helix	331-347	17
β-strand	352-354	3	5
α-helix	355-356	2
β-strand	362-364	3	5
α-helix	366-368	3
α-helix	369-379	11
α-helix	383-391	9
β-strand	392-394	3	6
β-strand	408-410	3	6
α-helix	413-440	28
β-strand	451-456	6	2
α-helix	468-485	18
α-helix	486-490	5
α-helix	491-498	8
α-helix	503-505	3
α-helix	512-519	8
α-helix	525-534	10
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
β-strand	598	1	8
α-helix	600-602	3
α-helix	603-610	8
α-helix	615-620	6
β-strand	642	1	8
α-helix	643-659	17
β-strand	662-669	8	2
α-helix	682-691	10
α-helix	698-702	5
β-strand	707-710	4	9
α-helix	711-719	9
α-helix	724-727	4
α-helix	731-741	11
β-strand	749-751	3	9
β-strand	755-758	4	9
α-helix	763-770	8
α-helix	774-788	15

Chain C: 46 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
β-strand	15-24	10	10
β-strand	28-33	6	10
β-strand	41-44	4	10
α-helix	45-47	3
β-strand	49-50	2	10
β-strand	61	1	11
α-helix	62-64	3
α-helix	70-82	13
β-strand	87-90	4	11
β-strand	93-97	5	11
α-helix	109-115	7
α-helix	118-119	2
α-helix	127-141	15
β-strand	145-150	6	11
α-helix	157-172	16
α-helix	177-184	8
α-helix	186-193	8
β-strand	194-195	2	12
β-strand	203-204	2	12
β-strand	207-214	8	11
β-strand	220-228	9	11
α-helix	233-235	3
β-strand	245	1	12
α-helix	246-254	9
α-helix	257-262	6
α-helix	268-270	3
α-helix	280-281	2
β-strand	282	1	13
α-helix	285-290	6
α-helix	293-295	3
α-helix	298-303	6
β-strand	306	1	13
α-helix	313-327	15
α-helix	331-347	17
β-strand	352-354	3	14
β-strand	362-364	3	14
α-helix	366-368	3
α-helix	369-378	10
α-helix	383-391	9
β-strand	392-395	4	15
β-strand	407-410	4	15
α-helix	411-412	2
α-helix	413-440	28
β-strand	450-456	7	11
α-helix	457-459	3
α-helix	468-484	17
α-helix	485-490	6
α-helix	491-498	8
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	16
α-helix	560-562	3
α-helix	566-568	3
α-helix	573-575	3
β-strand	576-581	6	16
β-strand	584-589	6	16
α-helix	593-596	4
β-strand	598	1	17
α-helix	603-610	8
α-helix	615-620	6
β-strand	642	1	17
α-helix	643-659	17
β-strand	662-669	8	11
α-helix	682-691	10
α-helix	694-701	8
β-strand	707-710	4	18
α-helix	711-718	8
α-helix	724-727	4
α-helix	731-741	11
β-strand	749-751	3	18
β-strand	755-758	4	18
α-helix	763-770	8
α-helix	774-787	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Unconventional myosin-VI	A, C	protein	788	Sus scrofa	F1RQI7 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4PFP_1 Unconventional myosin-VI (chains A, C)
EDGKPVWAPHPTDGFQVGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVED
NCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLG
TMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIDDR
IVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKE
ERNYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYL
KAGSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSGG
CNLKNKSTQALEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNARD
ALAKTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQ
QFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQ
HFTSAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDAL
HMSLESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRST
GASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGFPSRASFHELYNMYKKY
MPDKLARLDPRLFCKALFKALGLNEIDYKFGLTKVFFRPGKFAEFDQIMKSDPDHLAELV
KRVNHWLI

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
PGO	S-1,2-propanediol	C3 H8 O2	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MG	Magnesium ion	Mg	2

Primary citation

How actin initiates the motor activity of Myosin. Llinas, P., Isabet, T., Song, L. et al. Dev Cell (2015) 33:401-412. DOI 10.1016/j.devcel.2015.03.025 · PubMed

Other PDB entries of the same protein (UniProt F1RQI7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4PFO 1.75 Å, Myosin VI motor domain in the Pi release state, space group P212121
4PJN 2.0 Å, Myosin VI motor domain in the Pi release state, space group P212121 - shortly soaked…
4PJM 2.05 Å, Myosin VI motor domain in the Pi release state, space group P212121 - soaked with PO4 -…
4PJL 2.1 Å, Myosin VI motor domain A458E mutant in the Pi release state, space group P212121 -
4E7S 2.25 Å, Myosin VI D23R I24R R569E (MD) pre-powerstroke state
4E7Z 2.3 Å, Myosin VI (MD) pre-powerstroke state, P21 crystal form
4PJJ 2.4 Å, MYOSIN VI (MD-INSERT2-CAM, DELTA-INSERT1) post-rigor state - long soaking with PO4
4PK4 2.78 Å, Myosin VI motor domain in the PPS state - from a Pi release state crystal, space group…

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