5OGW: Actin-1

Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution. Determined by electron microscopy at 3.8 Å resolution. Released 27 Sept 2017.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Plasmodium falciparum (isolate HB3)
Chains: 5
Atoms: 14,736
Mol. weight: 214.62 kDa
Ligands: 9UE, MG, ADP
Released: 27 Sept 2017

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

Secondary structure: helices and β-sheets

5OGW contains 110 α-helices and 113 β-strands across 5 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.

Chains A and C: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	1
β-strand	20-24	5	1
β-strand	32-34	3	1
β-strand	38-41	4	2
α-helix	44	1
β-strand	45	1	3
β-strand	56-57	2	2
α-helix	59-63	5
β-strand	68-71	4	2
β-strand	74-75	2	4
β-strand	78-79	2	4
α-helix	82-90	9
α-helix	91-96	6
β-strand	106-110	5	1
α-helix	116-127	12
β-strand	134-139	6	1
α-helix	140-147	8
β-strand	155-158	4	5
β-strand	163-166	4	5
β-strand	168-169	2	6
β-strand	172-173	2	6
β-strand	179-181	3	5
α-helix	185-196	12
α-helix	197-199	3
α-helix	206-219	14
β-strand	221	1	7
α-helix	226-232	7
β-strand	241-244	4	8
β-strand	250-253	4	8
α-helix	256-259	4
α-helix	261-264	4
α-helix	277-286	10
α-helix	293-299	7
β-strand	301-303	3	5
α-helix	305-308	4
β-strand	310	1	7
α-helix	312-323	12
α-helix	329-330	2
β-strand	333	1	5
α-helix	341-350	10
α-helix	355-357	3
α-helix	359	1
β-strand	360-361	2	1
α-helix	362-368	7
α-helix	370-375	6

Chains B and D: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	9
β-strand	20-24	5	9
β-strand	32-34	3	9
β-strand	38-41	4	10
α-helix	44-45	2
β-strand	56-57	2	10
α-helix	59-63	5
β-strand	68-71	4	10
β-strand	74-75	2	11
β-strand	78-79	2	11
α-helix	82-90	9
α-helix	91-96	6
β-strand	106-110	5	9
α-helix	116-127	12
β-strand	134-139	6	9
α-helix	140-147	8
β-strand	155-158	4	12
β-strand	163-166	4	12
β-strand	168-169	2	3
β-strand	172-173	2	3
β-strand	179-181	3	12
α-helix	185-196	12
α-helix	197-199	3
α-helix	206-219	14
β-strand	221	1	13
α-helix	226-232	7
β-strand	241-244	4	14
β-strand	250-253	4	14
α-helix	256-259	4
α-helix	261-264	4
α-helix	277-286	10
α-helix	293-299	7
β-strand	301-303	3	12
α-helix	305-308	4
β-strand	310	1	13
α-helix	312-323	12
α-helix	329-330	2
β-strand	333	1	12
α-helix	341-350	10
α-helix	355-357	3
α-helix	359	1
β-strand	360-361	2	9
α-helix	362-368	7
α-helix	370-375	6

Chain E: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	29
β-strand	20-24	5	29
β-strand	32-34	3	29
β-strand	38-41	4	30
α-helix	44	1
β-strand	45	1	26
β-strand	56-57	2	30
α-helix	59-63	5
β-strand	68-71	4	30
β-strand	74-75	2	31
β-strand	78-79	2	31
α-helix	82-90	9
α-helix	91-96	6
β-strand	106-110	5	29
α-helix	116-127	12
β-strand	134-139	6	29
α-helix	140-147	8
β-strand	155-158	4	32
β-strand	163-166	4	32
β-strand	168-169	2	33
β-strand	172-173	2	33
β-strand	179-181	3	32
α-helix	185-196	12
α-helix	197-199	3
α-helix	206-219	14
β-strand	221	1	34
α-helix	226-232	7
β-strand	241-244	4	35
β-strand	250-253	4	35
α-helix	256-259	4
α-helix	261-264	4
α-helix	277-286	10
α-helix	293-299	7
β-strand	301-303	3	32
α-helix	305-308	4
β-strand	310	1	34
α-helix	312-323	12
α-helix	329-330	2
β-strand	333	1	32
α-helix	341-350	10
α-helix	355-357	3
α-helix	359	1
β-strand	360-361	2	29
α-helix	362-368	7
α-helix	370-374	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-1	A, B, C, D, E	protein	378	Plasmodium falciparum (isolate HB3)	Q8I4X0 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>5OGW_1 Actin-1 (chains A, B, C, D, E)
GAMGEEDVQALVVDNGSGNVKAGVAGDDAPRSVFPSIVGRPKNPGIMVGMEEKDAFVGDE
AQTKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRAAPEEHPVLLTEAPLNPKGNRE
RMTQIMFESFNVPAMYVAIQAVLSLYSSGRTTGIVLDSGDGVSHTVPIYEGYALPHAIMR
LDLAGRDLTEYLMKILHERGYGFSTSAEKEIVRDIKEKLCYIALNFDEEMKTSEQSSDIE
KSYELPDGNIITVGNERFRCPEALFQPSFLGKEAAGIHTTTFNSIKKCDVDIRKDLYGNI
VLSGGTTMYEGIGERLTRDITTLAPSTMKIKVVAPPERKYSVWIGGSILSSLSTFQQMWI
TKEEYDESGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
9UE	Jasplakinolide	C36 H45 Br N4 O6	3
MG	Magnesium ion	Mg	5
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

Primary citation

Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability. Pospich, S., Kumpula, E.P., von der Ecken, J. et al. Proc Natl Acad Sci U S A (2017) 114:10636-10641. DOI 10.1073/pnas.1707506114 · PubMed

Other PDB entries of the same protein (UniProt Q8I4X0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6I4E 1.22 Å, Crystal Structure of Plasmodium falciparum actin I in the Mg-ADP state
6I4D 1.24 Å, Crystal Structure of Plasmodium falciparum actin I in the Mg-K-ATP/ADP state
4CBU 1.3 Å, Crystal structure of Plasmodium falciparum actin I
5MVV 1.4 Å, Crystal structure of Plasmodium falciparum actin I- gelsolin segment 1 -CdATP complex
6I4H 1.4 Å, Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Ca-ATP state
6I4F 1.5 Å, Crystal Structure of Plasmodium falciparum actin I (A272W mutant) in the Mg-K-ATP/ADP…
6I4J 1.5 Å, Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Mg-ADP state
6I4K 1.83 Å, Crystal Structure of Plasmodium falciparum actin I (G115A mutant) in the Ca-ATP state
6I4L 1.83 Å, Crystal Structure of Plasmodium falciparum actin I (G115A mutant) in the Mg-K-ATP/ADP…
6I4I 1.9 Å, Crystal Structure of Plasmodium falciparum actin I (F54Y mutant) in the Mg-K-ADP-AlFn…
6I4G 2.0 Å, Crystal Structure of Plasmodium falciparum actin I (H74Q) in the Mg-K-ATP state
6TU4 2.6 Å, Structure of Plasmodium Actin1 filament

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