9L2N: Cytochalasin D

Crystal structure of Cytochalasin D bound to a filamentous conformation actin. Determined by X-ray diffraction at 1.7 Å resolution. Released 2 Jul 2025.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Gallus gallus, Physarum polycephalum
Chains: 2
Atoms: 4,941
Mol. weight: 61.53 kDa
Ligands: CA, CY9, MG, PO4
Released: 2 Jul 2025

Explore 9L2N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L2N contains 33 α-helices and 28 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: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-262	10
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	338-347	10
α-helix	350-354	5
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
α-helix	34-36	3
β-strand	44-51	8	7
β-strand	54-57	4	7
α-helix	58-59	2
α-helix	60-62	3
β-strand	65-67	3	8
β-strand	71-78	8	7
β-strand	88-95	8	7
α-helix	101-117	17
β-strand	123-128	6	7
α-helix	134-137	4
β-strand	146-148	3	8
α-helix	152-154	3
α-helix	156	1
β-strand	157	1	2
α-helix	158-159	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A	protein	375	Gallus gallus	P68139 (AlphaFold model)
Actin-binding protein fragmin P	B	protein	162	Physarum polycephalum	Q94707 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9L2N_1 Actin, alpha skeletal muscle (chains A)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (B), FASTA

>9L2N_2 Actin-binding protein fragmin P (chains B)
GPMQKQKEYNIADSAIANLGTELEKKVKLEASQHEDAWKGAGKQVGVEIWRIQQFKVVPV
PKKHHGSFYTGDSYIVLSTYHPKTNPDKLAYDVHFWLGAFTTQDEAGTAAYKTVELDDYL
GGLPVQYREVQGYESERFLSLFPKGGLRILDGGVETGFHHVE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
CY9	(3S,3aR,4S,6S,6aR,7E,10S,12R,13E,15R,15aR)-3-benzyl-6,12-dihydroxy-4,10,12-trim…	C30 H37 N O6	1
MG	Magnesium ion	Mg	1
PO4	Phosphate ion	O4 P	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Water and common crystallization additives (EDO) are not listed.

Primary citation

Microscopic and structural observations of actin filament capping and severing by cytochalasin D. Mitani, T., Takeda, S., Oda, T. et al. Proc Natl Acad Sci U S A (2025) 122:e2502164122-e2502164122. DOI 10.1073/pnas.2502164122 · PubMed

Other PDB entries of the same protein (UniProt P68139 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W4Z 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (AMPPNP-form)
7W50 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-Pi-form)
7W51 1.2 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-form)
7W52 2.0 Å, Crystal structure of fragmin domain-1 (15-160) in complex with actin
1MDU 2.2 Å, Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1…
8D13 2.43 Å, Helical ADP-F-actin
8D14 2.51 Å, Helical ADP-Pi-F-actin
7R94 2.6 Å, T-Plastin-F-actin complex
8C4E 2.6 Å, F-actin decorated by SipA426-685
9JW0 2.69 Å, Structure of the N-terminal 3 domains (V1-V3) villin bound to actin
7YNE 2.7 Å, Crystal structure of fragmin domain-1 (1-160) in complex with G-form actin
8C4C 2.7 Å, F-actin decorated by SipA497-669

Browse structure collections

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