6BNP: Unconventional myosin-VI

CryoEM structure of MyosinVI-actin complex in the rigor (nucleotide-free) state. Determined by electron microscopy at 4.6 Å resolution. Released 10 Jan 2018.

Method: Electron microscopy
Resolution: 4.6 Å
Organisms: Sus scrofa, Oryctolagus cuniculus
Chains: 14
Atoms: 56,792
Mol. weight: 815.12 kDa
Ligands: MG, ADP
Released: 10 Jan 2018

Explore 6BNP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BNP contains 406 α-helices and 340 β-strands across 14 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: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	44
β-strand	16-21	6	44
β-strand	29-32	4	44
β-strand	35-38	4	45
β-strand	41-42	2	46
β-strand	53-54	2	45
α-helix	57-59	3
β-strand	65-68	4	45
β-strand	71-72	2	47
β-strand	75-76	2	47
α-helix	79-89	11
α-helix	90-94	5
β-strand	103-104	2	44
β-strand	105-107	3	48
α-helix	111-112	2
α-helix	117-127	11
β-strand	131-132	2	49
β-strand	134-136	3	48
α-helix	137-145	9
β-strand	150-156	7	50
β-strand	159-166	8	50
β-strand	169-170	2	50
α-helix	172-174	3
β-strand	176-178	3	50
α-helix	183-194	12
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	51
β-strand	247-250	4	51
α-helix	252-259	8
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-300	4	50
α-helix	302-304	3
α-helix	311-320	10
α-helix	322	1
β-strand	329-330	2	50
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-355	4
β-strand	357-358	2	49
α-helix	359-365	7
α-helix	367-369	3

Chain B: 23 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	52
β-strand	17-21	5	52
β-strand	29-31	3	52
β-strand	35-38	4	53
β-strand	42	1	54
β-strand	53-54	2	53
β-strand	65-68	4	53
β-strand	71-72	2	55
β-strand	75-76	2	55
α-helix	79-89	11
α-helix	90-94	5
α-helix	98-100	3
β-strand	103-104	2	52
β-strand	105-107	3	56
α-helix	111-112	2
α-helix	117-127	11
β-strand	131-132	2	57
β-strand	134-136	3	56
α-helix	137-145	9
β-strand	149-152	4	58
β-strand	155-156	2	59
β-strand	159-162	4	59
β-strand	163-166	4	58
β-strand	169-170	2	58
α-helix	172-174	3
β-strand	176-178	3	59
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	60
β-strand	247-250	4	60
α-helix	252-259	8
α-helix	264-266	3
α-helix	274-282	9
α-helix	290-293	4
β-strand	297-298	2	58
α-helix	302-304	3
β-strand	307	1	61
β-strand	309	1	61
α-helix	311-320	10
α-helix	322	1
β-strand	329-330	2	58
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	57
α-helix	359-365	7
α-helix	367-369	3

Chain C: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	62
β-strand	17-21	5	62
β-strand	29-31	3	62
β-strand	35-38	4	63
β-strand	42	1	64
β-strand	53-54	2	63
α-helix	57-59	3
β-strand	65-68	4	63
β-strand	71-72	2	65
β-strand	75-76	2	65
α-helix	79-89	11
α-helix	90-94	5
α-helix	98-100	3
β-strand	103-104	2	62
β-strand	105-107	3	66
α-helix	115-127	13
β-strand	131-132	2	67
β-strand	134-136	3	66
α-helix	137-145	9
β-strand	150-152	3	46
β-strand	155-156	2	68
β-strand	159-162	4	68
β-strand	163-166	4	46
β-strand	169-170	2	46
β-strand	176-178	3	68
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	69
β-strand	247-250	4	69
α-helix	252-259	8
α-helix	264-266	3
α-helix	271-273	3
α-helix	274-282	9
α-helix	290-293	4
β-strand	297-298	2	46
α-helix	302-304	3
α-helix	311-320	10
β-strand	329-330	2	46
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-355	4
β-strand	357-358	2	67
α-helix	359-365	7

Chain D: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	70
β-strand	16-21	6	70
β-strand	29-32	4	70
β-strand	35-38	4	71
β-strand	42	1	72
β-strand	53-54	2	71
α-helix	57-60	4
β-strand	65-68	4	71
β-strand	71-72	2	73
β-strand	75-76	2	73
α-helix	79-89	11
α-helix	90-94	5
β-strand	103-104	2	70
β-strand	105-107	3	74
α-helix	111-112	2
α-helix	117-127	11
β-strand	131-132	2	75
β-strand	134-136	3	74
α-helix	137-144	8
β-strand	150-156	7	54
β-strand	159-166	8	54
β-strand	169-170	2	54
β-strand	176-178	3	54
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	76
β-strand	247-250	4	76
α-helix	252-259	8
α-helix	264-266	3
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-300	4	54
α-helix	302-304	3
α-helix	311-320	10
β-strand	329-330	2	54
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	75
α-helix	359-365	7

Chain E: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	77
β-strand	17-21	5	77
β-strand	29-31	3	77
β-strand	35-38	4	78
β-strand	42	1	79
β-strand	53-54	2	78
α-helix	57-60	4
β-strand	65-68	4	78
β-strand	71-72	2	80
β-strand	75-76	2	80
α-helix	79-92	14
α-helix	98-100	3
β-strand	102-107	6	77
α-helix	117-127	11
β-strand	131-136	6	77
α-helix	137-144	8
β-strand	149-152	4	64
β-strand	156	1	81
β-strand	159	1	81
β-strand	160-162	3	82
β-strand	163-166	4	64
β-strand	169-170	2	64
β-strand	176-178	3	82
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	83
β-strand	247-250	4	83
α-helix	253-259	7
α-helix	264-266	3
α-helix	274-282	9
α-helix	287-289	3
α-helix	290-293	4
β-strand	297-298	2	64
α-helix	311-320	10
α-helix	322	1
β-strand	329-330	2	64
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	77
α-helix	359-365	7
α-helix	367-370	4

Chain F: 21 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	84
β-strand	16-21	6	84
β-strand	29-32	4	84
β-strand	35-38	4	85
α-helix	41	1
β-strand	42	1	86
β-strand	53-54	2	85
α-helix	57-59	3
β-strand	65-68	4	85
β-strand	71-72	2	87
β-strand	75-76	2	87
α-helix	79-89	11
α-helix	90-94	5
β-strand	103-104	2	84
β-strand	105-107	3	88
α-helix	111-112	2
α-helix	117-127	11
β-strand	131-132	2	89
β-strand	134-136	3	88
α-helix	137-144	8
β-strand	149-152	4	72
β-strand	155-156	2	90
β-strand	159-162	4	90
β-strand	163-166	4	72
β-strand	169-170	2	72
β-strand	176-178	3	90
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	91
β-strand	247-250	4	91
α-helix	252-259	8
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-298	2	72
α-helix	302-304	3
α-helix	311-320	10
α-helix	328	1
β-strand	329-330	2	72
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	89
α-helix	359-365	7

Chain G: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	92
β-strand	17-21	5	92
β-strand	29-31	3	92
β-strand	35-38	4	93
β-strand	53-54	2	93
α-helix	57-59	3
β-strand	65-68	4	93
β-strand	71-72	2	94
β-strand	75-76	2	94
α-helix	79-89	11
α-helix	90-94	5
α-helix	98-100	3
β-strand	103-104	2	92
β-strand	105-107	3	95
α-helix	111-112	2
α-helix	117-127	11
β-strand	131-132	2	96
β-strand	134-136	3	95
α-helix	137-145	9
β-strand	150-156	7	79
β-strand	159-166	8	79
β-strand	169-170	2	79
α-helix	172-174	3
β-strand	176-178	3	79
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	97
β-strand	247-250	4	97
α-helix	252-256	5
α-helix	258-260	3
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-298	2	79
α-helix	302-304	3
α-helix	311-320	10
β-strand	329-330	2	79
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	96
α-helix	359-365	7

Chain H: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	98
β-strand	17-21	5	98
β-strand	29-31	3	98
β-strand	35-38	4	99
β-strand	53-54	2	99
α-helix	57-60	4
β-strand	65-68	4	99
β-strand	71-72	2	100
β-strand	75-76	2	100
α-helix	79-89	11
α-helix	90-94	5
α-helix	98-100	3
β-strand	103-107	5	98
α-helix	111-112	2
α-helix	115-127	13
β-strand	131-132	2	101
β-strand	134-136	3	98
α-helix	137-144	8
β-strand	150-152	3	86
β-strand	155-156	2	102
β-strand	159-162	4	102
β-strand	163-166	4	86
β-strand	169-170	2	86
α-helix	172-174	3
β-strand	176-178	3	102
α-helix	183-193	11
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-231	9
β-strand	238-241	4	103
β-strand	247-250	4	103
α-helix	252-259	8
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-298	2	86
β-strand	307	1	104
β-strand	309	1	104
α-helix	311-320	10
β-strand	329-330	2	86
α-helix	335-337	3
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	101
α-helix	359-365	7
α-helix	367-369	3

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Unconventional myosin-VI	I, J, K, L, M, N	protein	704	Sus scrofa	Q29122 (AlphaFold model)
Actin, alpha skeletal muscle	A, B, C, D, E, F, G, H	protein	373	Oryctolagus cuniculus	P68135 (AlphaFold model)

Sequence of entity 1 (I, J, K, L, M, N), FASTA

>6BNP_1 Unconventional myosin-VI (chains I, J, K, L, M, N)
EDGKPVWAPHPTDGFQVGNIVDIGPDSLTIEPLNQKGKTFLALINQVFPAEEDSKKDVED
NCSLMYLNEATLLHNIKVRYSKDRIYTYVANILIAVNPYFDIPKIYSSETIKSYQGKSLG
TMPPHVFAIADKAFRDMKVLKLSQSIIVSGESGAGKTENTKFVLRYLTESYGTGQDIDDR
IVEANPLLEAFGNAKTVRNNNSSRFGKFVEIHFNEKSSVVGGFVSHYLLEKSRICVQGKE
ERNYHIFYRLCAGASEDIRERLHLSSPDNFRYLNRGCTRYFANKETDKQILQNRKSPEYL
KAGSLKDPLLDDHGDFIRMCTAMKKIGLDDEEKLDLFRVVAGVLHLGNIDFEEAGSTSGG
CNLKNKSTQALEYCAELLGLDQDDLRVSLTTRVMLTTAGGAKGTVIKVPLKVEQANNARD
ALAKTVYSHLFDHVVNRVNQCFPFETSSYFIGVLDIAGFEYFEHNSFEQFCINYCNEKLQ
QFFNERILKEEQELYQKEGLGVNEVHYVDNQDCIDLIEARLVGILDILDEENRLPQPSDQ
HFTSAVHQKHKDHFRLSIPRKSKLAIHRNIRDDEGFIIRHFAGAVCYETTQFVEKNNDAL
HMSLESLICESRDKFIRELFESSTNNNKDTKQKAGKLSFISVGNKFKTQLNLLLDKLRST
GASFIRCIKPNLKMTSHHFEGAQILSQLQCSGMVSVLDLMQGGF

Sequence of entity 2 (A, B, C, D, E, F, G, H), FASTA

>6BNP_2 Actin, alpha skeletal muscle (chains A, B, C, D, E, F, G, H)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	8

Primary citation

Cryo-EM structures reveal specialization at the myosin VI-actin interface and a mechanism of force sensitivity. Gurel, P.S., Kim, L.Y., Ruijgrok, P.V. et al. Elife (2017) 6. DOI 10.7554/eLife.31125 · 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
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

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