9FJY: Actin, cytoplasmic 1, N-terminally processed

Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2). Determined by electron microscopy at 3.79 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 3.79 Å
Organisms: Bos taurus, Amanita phalloides
Chains: 10
Atoms: 15,968
Mol. weight: 235.77 kDa
Ligands: MG, PO4, ADP
Released: 11 Sept 2024

Explore 9FJY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FJY contains 108 α-helices and 122 β-strands across 6 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: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	53-54	2	2
α-helix	56-60	5
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-132	2	4
β-strand	134-136	3	1
α-helix	137-145	9
β-strand	150-155	6	5
β-strand	160-165	6	5
β-strand	176-178	3	5
α-helix	182-196	15
α-helix	203-205	3
α-helix	206-213	8
α-helix	223-231	9
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-284	11
α-helix	287-295	9
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	309-320	12
β-strand	330	1	5
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-353	3
α-helix	356	1
β-strand	357-358	2	4
α-helix	359-365	7
α-helix	367-371	5

Chain B: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-10	3	7
β-strand	16-20	5	7
β-strand	29-32	4	7
β-strand	35-38	4	8
β-strand	53-54	2	8
α-helix	56-60	5
β-strand	65-68	4	8
β-strand	71-72	2	9
β-strand	75-76	2	9
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-125	13
β-strand	131-136	6	7
α-helix	140-145	6
β-strand	149	1	10
β-strand	151-155	5	11
β-strand	160-163	4	11
β-strand	166	1	10
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	182-196	15
α-helix	206-216	11
α-helix	223-231	9
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-295	6
β-strand	297-301	5	11
α-helix	303-305	3
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	11
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	367-371	5

Chain C: 21 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
β-strand	16	1	14
β-strand	17-21	5	13
β-strand	29	1	13
β-strand	32	1	14
β-strand	35-38	4	15
β-strand	53-54	2	15
α-helix	56-60	5
β-strand	65-68	4	15
β-strand	71-72	2	16
β-strand	75-76	2	16
α-helix	82-88	7
α-helix	89-93	5
β-strand	103-107	5	13
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	13
α-helix	137-145	9
β-strand	150	1	17
β-strand	151-155	5	18
β-strand	160-162	3	18
β-strand	165-166	2	17
β-strand	169-170	2	17
α-helix	172-174	3
β-strand	176-178	3	18
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	19
β-strand	247-250	4	19
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	18
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	18
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	366-371	6

Chain D: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	20
β-strand	16-20	5	20
β-strand	29-32	4	20
β-strand	35-36	2	21
β-strand	37-38	2	22
β-strand	53-54	2	21
α-helix	56-60	5
β-strand	65-66	2	22
β-strand	71-72	2	23
β-strand	75-76	2	23
α-helix	79-87	9
α-helix	88-93	6
β-strand	103-107	5	20
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	20
α-helix	137-145	9
β-strand	150-154	5	24
β-strand	160-166	7	24
β-strand	169-170	2	24
β-strand	176-178	3	24
α-helix	182-196	15
α-helix	203-215	13
α-helix	223-230	8
β-strand	238-241	4	25
β-strand	247-250	4	25
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	296-300	5	24
α-helix	302-304	3
α-helix	309-320	12
β-strand	328-330	3	24
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	20
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	26
β-strand	11	1	27
α-helix	13-17	5
α-helix	19-31	13
β-strand	34-37	4	26
β-strand	40	1	27
α-helix	46-56	11
β-strand	64	1	26
β-strand	67	1	26
β-strand	72	1	28
β-strand	81-84	4	26
β-strand	91-96	6	29
β-strand	111	1	28
β-strand	114-119	6	29
β-strand	127-134	8	29
α-helix	140-157	18
β-strand	162-168	7	29
α-helix	185-188	4
β-strand	193-194	2	29
β-strand	203	1	30
β-strand	212	1	29
β-strand	215-217	3	29
α-helix	219-224	6
β-strand	225	1	31
α-helix	226	1
β-strand	231-232	2	26
α-helix	235-238	4
α-helix	243-249	7
β-strand	252	1	30
β-strand	255-258	4	26
β-strand	259	1	31

Chain F: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	32
β-strand	11	1	33
α-helix	13-17	5
α-helix	20-30	11
β-strand	34-36	3	32
β-strand	40	1	33
α-helix	47-55	9
β-strand	64-66	3	32
β-strand	82-84	3	32
β-strand	89-96	8	34
β-strand	114-120	7	34
β-strand	127-134	8	34
α-helix	140-157	18
β-strand	164-168	5	34
α-helix	178-183	6
β-strand	193-194	2	34
β-strand	203	1	35
β-strand	212-216	5	34
α-helix	219-224	6
β-strand	225	1	36
α-helix	226	1
β-strand	231-232	2	32
α-helix	235-238	4
α-helix	243-249	7
β-strand	252	1	35
β-strand	255-258	4	32
β-strand	259	1	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 1, N-terminally processed	A, B, C, D	protein	374	Bos taurus	P60712 (AlphaFold model)
Deoxyribonuclease-1	E, F	protein	282	Bos taurus	P00639 (AlphaFold model)
Phalloidin	G, H, I, J	protein	7	Amanita phalloides

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

>9FJY_1 Actin, cytoplasmic 1, N-terminally processed (chains A, B, C, D)
DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSK
RGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQ
IMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLA
GRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYE
LPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
YDESGPSIVHRKCF

Sequence of entity 2 (E, F), FASTA

>9FJY_2 Deoxyribonuclease-1 (chains E, F)
MRGTRLMGLLLALAGLLQLGLSLKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQ
EVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYD
DGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKW
HLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAG
SLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT

Sequence of entity 3 (G, H, I, J), FASTA

>9FJY_3 Phalloidin (chains G, H, I, J)
WXATCPA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
PO4	Phosphate ion	O4 P	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4

Primary citation

Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly. Boiero Sanders, M., Oosterheert, W., Hofnagel, O. et al. Nat Commun (2024) 15:7969-7969. DOI 10.1038/s41467-024-52251-3 · PubMed

Other PDB entries of the same protein (UniProt P60712 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3UB5 2.2 Å, Profilin:actin with a wide open nucleotide cleft
3U4L 2.4 Å, Cryocooled bovine profilin:actin crystal structure to 2.4 A
2BTF 2.55 Å, The structure of crystalline profilin-beta-actin
2OAN 2.61 Å, Structure of oxidized beta-actin
1HLU 2.65 Å, Structure of bovine beta-actin-profilin complex with actin bound ATP phosphates solvent…
8OI6 3.59 Å, Cryo-EM structure of the undecorated barbed end of filamentous beta/gamma actin
7PDZ 3.8 Å, Structure of capping protein bound to the barbed end of a cytoplasmic actin filament
9FJU 3.84 Å, Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 1)

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