1DFK: Myosin head

Nucleotide-free scallop myosin S1-near rigor state. Determined by X-ray diffraction at 4.2 Å resolution. Released 25 Oct 2000.

Method: X-ray diffraction
Resolution: 4.2 Å
Organism: Argopecten irradians
Chains: 3
Atoms: 5,032
Mol. weight: 127.82 kDa
Ligands: CA
Released: 25 Oct 2000

Explore 1DFK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1DFK contains 54 α-helices and 29 β-strands across 3 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: 38 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	33-37	5	1
β-strand	43-50	8	1
β-strand	55-60	6	1
β-strand	66-70	5	1
α-helix	71-73	3
β-strand	75	1	1
α-helix	80-82	3
β-strand	87	1	2
α-helix	88-90	3
α-helix	96-107	12
β-strand	113-116	4	2
β-strand	119-123	5	2
α-helix	134-140	7
α-helix	152-162	11
α-helix	163-167	5
β-strand	169-176	8	2
α-helix	182-195	14
α-helix	217-220	4
α-helix	222-229	8
β-strand	244-251	8	2
β-strand	257-265	9	2
α-helix	270-272	3
α-helix	294-296	3
α-helix	297-300	4
α-helix	306-308	3
α-helix	310-312	3
α-helix	324-337	14
α-helix	344-358	15
β-strand	363	1	3
β-strand	374	1	3
α-helix	378-386	9
α-helix	391-399	9
α-helix	417-444	28
β-strand	454-460	7	2
β-strand	470	1	4
α-helix	472-503	32
α-helix	513-515	3
α-helix	517-524	8
α-helix	529-537	9
α-helix	544-555	12
β-strand	562-563	2	4
β-strand	578-582	5	4
β-strand	585-589	5	4
α-helix	594-599	6
α-helix	606-609	4
α-helix	610-612	3
α-helix	616-621	6
α-helix	645-660	16
β-strand	663-671	9	2
α-helix	684-693	10
α-helix	696-705	10
β-strand	710-712	3	5
α-helix	713-720	8
α-helix	738-745	8
β-strand	753-754	2	5
β-strand	759-762	4	5
α-helix	766-796	31
α-helix	800-820	21
α-helix	825-833	9

Chain Y: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	15-27	13
α-helix	37-45	9
α-helix	53-60	8
α-helix	69-77	9
α-helix	86-94	9
β-strand	104-105	2	6
α-helix	106-115	10
α-helix	122-129	8
β-strand	134	1	6
β-strand	138-139	2	6
α-helix	141-148	8

Chain Z: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-21	17
β-strand	28-29	2	7
α-helix	33-39	7
α-helix	46-52	7
β-strand	62-63	2	7
α-helix	65-74	10
α-helix	83-91	9
β-strand	102	1	8
α-helix	103-112	10
α-helix	119-129	11
β-strand	138	1	8
α-helix	141-150	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Myosin head	A	protein	830	Argopecten irradians	P24733 (AlphaFold model)
Myosin head	Y	protein	139	Argopecten irradians	P13543 (AlphaFold model)
Myosin head	Z	protein	152	Argopecten irradians	P07291 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1DFK_1 MYOSIN HEAD (chains A)
SDPDFQYLAVDRKKLMKEQTAAFDGKKNCWVPDEKEGFASAEIQSSKGDEITVKIVADSS
TRTVKKDDIQSMNPPKFEKLEDMANMTYLNEASVLYNLRSRYTSGLIYTYSGLFCIAVNP
YRRLPIYTDSVIAKYRGKRKTEIPPHLFSVADNAYQNMVTDRENQSCLITGESGAGKTEN
TKKVIMYLAKVACAVKKKDEEASDKKEGSLEDQIIQANPVLEAYGNAKTTRNNNSSRFGK
FIRIHFGPTGKIAGADIETYLLEKSRVTYQQSAERNYHIFYQICSNAIPELNDVMLVTPD
SGLYSFINQGCLTVDNIDDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEMKFKQ
RPREEQAESDGTAEAEKVAFLCGINAGDLLKALLKPKVKVGTEMVTKGQNMNQVVNSVGA
LAKSLYDRMFNWLVRRVNKTLDTKAKRNYYIGVLDIAGFEIFDFNSFEQLCINYTNERLQ
QFFNHHMFILEQEEYKKEGIAWEFIDFGMDLQMCIDLIEKPMGILSILEEECMFPKADDK
SFQDKLYQNHMGKNRMFTKPGKPTRPNQGPAHFELHHYAGNVPYSITGWLEKNKDPINEN
VVALLGASKEPLVAELFKAPEEPAGGGKKKKGKSSAFQTISAVHRESLNKLMKNLYSTHP
HFVRCIIPNELKQPGLVDAELVLHQLQCNGVLEGIRICRKGFPSRLIYSEFKQRYSILAP
NAIPQGFVDGKTVSEKILAGLQMDPAEYRLGTTKVFFKAGVLGNLEEMRDERLSKIISMF
QAHIRGYLIRKAYKKLQDQRIGLSVIQRNIRKWLVLRNWQWWKLYSKVKP

Sequence of entity 2 (Y), FASTA

>1DFK_2 MYOSIN HEAD (chains Y)
LPQKQIQEMKEAFSMIDVDRDGFVSKEDIKAISEQLGRAPDDKELTAMLKEAPGPLNFTM
FLSIFSDKLSGTDSEETIRNAFAMFDEQETKKLNIEYIKDLLENMGDNFNKDEMRMTFKE
APVEGGKFDYVKFTAMIKG

Sequence of entity 3 (Z), FASTA

>1DFK_3 MYOSIN HEAD (chains Z)
LSQDEIDDLKDVFELFDFWDGRDGAVDAFKLGDVCRCLGINPRNEDVFAVGGTHKMGEKS
LPFEEFLPAYEGLMDCEQGTFADYMEAFKTFDREGQGFISGAELRHVLTALGERLSDEDV
DEIIKLTDLQEDLEGNVKYEDFVKKVMAGPYP

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Three conformational states of scallop myosin S1. Houdusse, A., Szent-Gyorgyi, A.G., Cohen, C. Proc Natl Acad Sci U S A (2000) 97:11238-11243. DOI 10.1073/pnas.200376897 · PubMed

Other PDB entries of the same protein (UniProt P24733 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WDC 2.0 Å, Scallop myosin regulatory domain
3JVT 2.1 Å, Calcium-bound Scallop Myosin Regulatory Domain (Lever Arm) with Reconstituted Complete…
1KK8 2.3 Å, Scallop myosin (S1-ADP-befx) in the actin-detached conformation
3BAS 2.3 Å, Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (C2) form
3BAT 2.3 Å, Crystal structure of the N-terminal region of the scallop myosin rod, monoclinic (P21)…
1B7T 2.5 Å, Myosin digested by papain
1QVI 2.54 Å, Crystal structure of scallop myosin S1 in the pre-power stroke state to 2.6 Angstrom…
3JTD 2.57 Å, Calcium-free Scallop Myosin Regulatory Domain with ELC-D19A Point Mutation
1SR6 2.75 Å, Structure of nucleotide-free scallop myosin S1
1L2O 2.8 Å, Scallop myosin S1-ADP-p-pdm in the actin-detached conformation
1SCM 2.8 Å, Structure of the regulatory domain of scallop myosin at 2.8 Å resolution
1KQM 3.0 Å, Scallop myosin S1-amppnp in the actin-detached conformation

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