9Y9M: Capping protein

Capping protein bound to the barbed end of cofilactin. Determined by electron microscopy at 3.06 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 10
Atoms: 22,655
Mol. weight: 331.85 kDa
Ligands: ADP, MG
Released: 4 Mar 2026

Explore 9Y9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y9M contains 160 α-helices and 146 β-strands across 10 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 b: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	35
α-helix	9-19	11
β-strand	21	1	15
α-helix	26-30	5
β-strand	33-40	8	35
β-strand	46-56	11	35
α-helix	57-59	3
α-helix	67-73	7
β-strand	81-91	11	35
β-strand	94-104	11	35
α-helix	111-127	17
β-strand	133-136	4	35
α-helix	140-142	3
α-helix	146-152	7
α-helix	155-157	3
β-strand	158-161	4	35
β-strand	164-165	2	35

Chain A: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	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	55-60	6
β-strand	65-68	4	2
β-strand	71	1	3
β-strand	76	1	3
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	149-155	7	4
β-strand	160-166	7	4
β-strand	169-170	2	4
α-helix	172-174	3
β-strand	176-178	3	4
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-230	8
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	252-255	4
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	4
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain B: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	6
β-strand	16-21	6	6
β-strand	29-32	4	6
β-strand	35-38	4	7
β-strand	53-54	2	7
α-helix	55-60	6
β-strand	65-68	4	7
β-strand	71	1	8
β-strand	76	1	8
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	105-107	3	6
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-132	2	9
β-strand	134-136	3	6
α-helix	137-144	8
β-strand	149-155	7	10
β-strand	160-166	7	10
β-strand	169-170	2	10
α-helix	172-174	3
β-strand	176-178	3	10
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-230	8
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	252-255	4
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	10
α-helix	303-305	3
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	10
α-helix	338-348	11
α-helix	350-352	3
β-strand	357-358	2	9
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain c: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	37
α-helix	9-19	11
β-strand	21	1	27
α-helix	26-30	5
β-strand	33-40	8	37
β-strand	46-56	11	37
α-helix	57-59	3
α-helix	60-64	5
α-helix	67-73	7
β-strand	81-91	11	37
β-strand	94-104	11	37
α-helix	111-127	17
β-strand	133-136	4	37
α-helix	140-142	3
α-helix	147-152	6
α-helix	155-157	3
β-strand	158-161	4	37
β-strand	164-165	2	37

Chain C: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
β-strand	53-54	2	13
α-helix	55-57	3
β-strand	65-68	4	13
β-strand	71	1	14
β-strand	76	1	14
α-helix	79-87	9
α-helix	88-93	6
β-strand	96	1	15
α-helix	98-100	3
β-strand	103-107	5	12
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	12
α-helix	137-144	8
β-strand	149-155	7	16
β-strand	160-166	7	16
β-strand	169-170	2	16
β-strand	176-178	3	16
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-230	8
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	252-254	3
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	291-294	4
β-strand	297-300	4	16
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	16
α-helix	335-337	3
α-helix	338-346	9
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain D: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	18
β-strand	16-21	6	18
β-strand	29-32	4	18
β-strand	35-38	4	19
β-strand	53-54	2	19
α-helix	56-61	6
β-strand	65-68	4	19
β-strand	71	1	20
β-strand	76	1	20
α-helix	79-87	9
α-helix	88-93	6
β-strand	96	1	21
α-helix	98-100	3
β-strand	103-107	5	18
α-helix	113-125	13
β-strand	131-136	6	18
α-helix	137-144	8
β-strand	149-155	7	22
β-strand	160-166	7	22
β-strand	169-170	2	22
β-strand	176-178	3	22
α-helix	182-196	15
α-helix	203-215	13
α-helix	223-232	10
β-strand	238-241	4	23
β-strand	247-250	4	23
α-helix	252-255	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-292	6
β-strand	297-300	4	22
α-helix	303-305	3
α-helix	309-319	11
β-strand	329-330	2	22
α-helix	335-337	3
α-helix	338-346	9
α-helix	350-352	3
β-strand	357-358	2	18
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain E: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	8-12	5	24
β-strand	17-21	5	24
β-strand	29-31	3	24
β-strand	35-37	3	25
β-strand	53-54	2	25
α-helix	58-60	3
α-helix	62-64	3
β-strand	66-68	3	25
β-strand	71	1	26
β-strand	76	1	26
α-helix	79-87	9
α-helix	88-93	6
β-strand	96	1	27
α-helix	98-100	3
β-strand	103-107	5	24
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	24
α-helix	137-144	8
β-strand	150-155	6	28
β-strand	160-166	7	28
β-strand	169-170	2	28
β-strand	176-178	3	28
α-helix	182-193	12
α-helix	204-216	13
α-helix	223-230	8
β-strand	238-241	4	29
β-strand	247-250	4	29
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	287-293	7
β-strand	297-300	4	28
α-helix	303-305	3
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	28
α-helix	335-337	3
α-helix	338-346	9
α-helix	353-355	3
β-strand	357-358	2	24
α-helix	359-365	7
α-helix	369-372	4

Chain Y: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	24-25	2
α-helix	29-40	12
α-helix	43-46	4
α-helix	51-60	10
β-strand	63-65	3	30
β-strand	74-76	3	30
β-strand	81	1	31
β-strand	86-89	4	31
β-strand	94-99	6	31
β-strand	104-110	7	31
α-helix	118-134	17
β-strand	136	1	32
β-strand	139-148	10	33
β-strand	151-164	14	33
β-strand	169-180	12	33
β-strand	185-198	14	33
β-strand	203-217	15	33
α-helix	221-249	29
α-helix	255-258	4
α-helix	271-274	4

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	376	Oryctolagus cuniculus	P68135 (AlphaFold model)
F-actin-capping protein subunit alpha-1	Y	protein	286	Homo sapiens	P52907 (AlphaFold model)
F-actin-capping protein subunit beta	Z	protein	272	Homo sapiens	P47756 (AlphaFold model)
Cofilin-2	a, b, c	protein	166	Homo sapiens	Q9Y281 (AlphaFold model)

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

>9Y9M_1 Actin, alpha skeletal muscle (chains A, B, C, D, E)
CDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKM
TQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLD
LAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKS
YELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVM
SGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITK
QEYDEAGPSIVHRKCF

Sequence of entity 2 (Y), FASTA

>9Y9M_2 F-actin-capping protein subunit alpha-1 (chains Y)
MADFDDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSW
RESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYXXXXXXXXX

Sequence of entity 3 (Z), FASTA

>9Y9M_3 F-actin-capping protein subunit beta (chains Z)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC

Sequence of entity 4 (a, b, c), FASTA

>9Y9M_4 Cofilin-2 (chains a, b, c)
MASGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLFCLSDDKRQIIVEEAKQILVGDI
GDTVEDPYTSFVKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASS
KDAIKKKFTGIKHEWQVNGLDDIKDRSTLGEKLGGNVVVSLEGKPL

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5
MG	Magnesium ion	Mg	5

Primary citation

Mechanisms of disassembly at the actin filament pointed and barbed ends. Palmer, N.J., Boczkowska, M., Rebowski, G. et al. Sci Adv (2026) 12:eaee5882-eaee5882. DOI 10.1126/sciadv.aee5882 · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

Browse structure collections

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