2AKA: Myosin II heavy chain

Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Aug 2005.

Method: X-ray diffraction
Resolution: 1.9 Å
Organisms: Dictyostelium discoideum, Rattus norvegicus
Chains: 3
Atoms: 9,377
Mol. weight: 123.25 kDa
Released: 23 Aug 2005

Explore 2AKA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AKA contains 50 α-helices and 44 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: 36 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	10-15	6
β-strand	34-37	4	1
β-strand	48-55	8	1
β-strand	59-63	5	1
β-strand	69-73	5	1
β-strand	78-79	2	1
α-helix	80-82	3
α-helix	83-85	3
β-strand	90	1	2
α-helix	91-93	3
α-helix	99-110	12
β-strand	116-119	4	2
β-strand	122-126	5	2
α-helix	137-143	7
α-helix	148-150	3
α-helix	155-169	15
β-strand	173-178	6	2
α-helix	185-199	15
α-helix	211-226	16
β-strand	227-228	2	3
β-strand	236-237	2	3
β-strand	240-247	8	2
β-strand	253-261	9	2
α-helix	265-268	4
β-strand	278	1	3
α-helix	279-287	9
α-helix	290-296	7
α-helix	301-303	3
α-helix	320-333	14
α-helix	338-355	18
β-strand	360-361	2	4
β-strand	366	1	5
β-strand	367-368	2	4
α-helix	373-382	10
α-helix	386-394	9
β-strand	397-400	4	6
β-strand	403-406	4	6
β-strand	410	1	5
α-helix	411-441	31
β-strand	448-454	7	2
α-helix	456-458	3
β-strand	464	1	7
α-helix	466-496	31
α-helix	506-510	5
α-helix	511-518	8
β-strand	520	1	8
β-strand	523	1	8
α-helix	525-531	7
α-helix	540-551	12
β-strand	558-559	2	7
β-strand	567-572	6	7
β-strand	575-580	6	7
α-helix	584-587	4
α-helix	594-601	8
α-helix	606-613	8
α-helix	630-646	17
β-strand	649-656	8	2
α-helix	669-678	10
α-helix	681-689	9
β-strand	694-697	4	9
α-helix	698-705	8
α-helix	706-708	3
α-helix	719-729	11
α-helix	734-736	3
β-strand	737-739	3	9
β-strand	743-746	4	9
α-helix	750-764	15

Chain B: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	24-25	2
β-strand	33-38	6	10
β-strand	39	1	11
α-helix	44-52	9
β-strand	69-75	7	10
β-strand	80-83	4	10
β-strand	91	1	10
α-helix	94-108	15
β-strand	120-126	7	10
β-strand	132-136	5	10
α-helix	138-139	2
β-strand	140	1	11
α-helix	152-164	13
β-strand	169-176	8	10
α-helix	181-183	3
α-helix	185-193	9
β-strand	200-205	6	10
α-helix	207-209	3
α-helix	211	1
α-helix	217-220	4
β-strand	231-233	3	10
β-strand	240	1	12
β-strand	246	1	12
α-helix	248-261	14
α-helix	266-271	6
α-helix	274-303	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
myosin II heavy chain	A	protein	776	Dictyostelium discoideum	P08799 (AlphaFold model)
Linker	L	protein	13
Dynamin-1	B	protein	299	Rattus norvegicus	P21575 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2AKA_1 myosin II heavy chain (chains A)
MHHHHHHHDGTENPIHDRTSDYHKYLKVKQGDSDLFKLTVSDKRYIWYNPDPKERDSYEC
GEIVSETSDSFTFKTVDGQDRQVKKDDANQRNPIKFDGVEDMSELSYLNEPAVFHNLRVR
YNQDLIYTYSGLFLVAVNPFKRIPIYTQEMVDIFKGRRRNEVAPHIFAISDVAYRSMLDD
RQNQSLLITGESGAGKTENTKKVIQYLASVAGRNQANGSGVLEQQILQANPILEAFGNAK
TTRNNNSSRFGKFIEIQFNSAGFISGASIQSYLLEKSRVVFQSETERNYHIFYQLLAGAT
AEEKKALHLAGPESFNYLNQSGCVDIKGVSDSEEFKITRQAMDIVGFSQEEQMSIFKIIA
GILHLGNIKFEKGAGEGAVLKDKTALNAASTVFGVNPSVLEKALMEPRILAGRDLVAQHL
NVEKSSSSRDALVKALYGRLFLWLVKKINNVLCQERKAYFIGVLDISGFEIFKVNSFEQL
CINYTNEKLQQFFNHHMFKLEQEEYLKEKINWTFIDFGLDSQATIDLIDGRQPPGILALL
DEQSVFPNATDNTLITKLHSHFSKKNAKYEEPRFSKTEFGVTHYAGQVMYEIQDWLEKNK
DPLQQDLELCFKDSSDNVVTKLFNDPNIASRAKKGANFITVAAQYKEQLASLMATLETTN
PHFVRCIIPNNKQLPAKLEDKVVLDQLRCNGVLEGIRITRKGFPNRIIYADFVKRYYLLA
PNVPRDAEDSQKATDAVLKHLNIDPEQYRFGITKIFFRAGQLARIEEAREQRISEI

Sequence of entity 2 (L), FASTA

>2AKA_2 LINKER (chains L)
TRLVPRGSELALE

Sequence of entity 3 (B), FASTA

>2AKA_3 Dynamin-1 (chains B)
MEDLIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVT
RRPLVLQLVNSTTEYAEFLHCKGKKFTDFEEVRLEIEAETDRVTGTNKGISPVPINLRVY
SPHVLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSD
ALKIAKEVDPQGQRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGK
KDITAALAAERKFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQL

Primary citation

Crystal structure of the GTPase domain of rat dynamin 1. Reubold, T.F., Eschenburg, S., Becker, A. et al. Proc Natl Acad Sci U S A (2005) 102:13093-13098. DOI 10.1073/pnas.0506491102 · PubMed

Other PDB entries of the same protein (UniProt P08799 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1W9I 1.75 Å, Myosin II Dictyostelium discoideum motor domain S456Y bound with MgADP-BeFx
3MYK 1.84 Å, Insights into the Importance of Hydrogen Bonding in the Gamma-Phosphate Binding Pocket…
6Z7T 1.88 Å, Nucleotide-free Myosin-II motor domain
1LVK 1.9 Å, X-ray crystal structure of the MG (DOT) 2'(3')-O-(N-methylanthraniloyl) nucleotide bound…
1VOM 1.9 Å, Complex between dictyostelium myosin and mgadp and vanadate at 1.9A resolution
1W9L 1.95 Å, Myosin II Dictyostelium discoideum motor domain S456E bound with MgADP-AlF4
1D0X 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with M-nitrophenyl…
1D0Y 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with O-nitrophenyl…
1D0Z 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with P-nitrophenyl…
1D1A 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with o,p-dinitrophenyl…
1D1B 2.0 Å, Dictyostelium myosin S1DC (motor domain fragment) complexed with o,p-dinitrophenyl…
1MMD 2.0 Å, Truncated head of myosin from dictyostelium discoideum complexed with mgadp-BEF3

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