9YIM: Capping protein

Capping protein bound to the barbed end of F-actin. Determined by electron microscopy at 2.62 Å resolution. Released 4 Mar 2026.

Method: Electron microscopy
Resolution: 2.62 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 7
Atoms: 19,039
Mol. weight: 271.67 kDa
Ligands: ADP, MG
Released: 4 Mar 2026

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

Secondary structure: helices and β-sheets

9YIM contains 140 α-helices and 123 β-strands across 7 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, 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	56-60	5
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	150-155	6	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	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
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	4
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-368	3
α-helix	370-373	4

Chain B: 25 helices, 19 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	56-60	5
α-helix	62-64	3
β-strand	65-68	4	7
β-strand	71-72	2	8
β-strand	75-76	2	8
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	6
α-helix	113-125	13
β-strand	131-136	6	6
α-helix	137-145	9
β-strand	150-155	6	9
β-strand	160-166	7	9
β-strand	169-170	2	9
α-helix	172-174	3
β-strand	176-178	3	9
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	10
β-strand	247-250	4	10
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
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	9
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	9
α-helix	338-347	10
β-strand	357-358	2	6
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	11
β-strand	16-21	6	11
β-strand	29-32	4	11
β-strand	35-38	4	12
β-strand	41-42	2	4
β-strand	53-54	2	12
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	12
β-strand	71-72	2	13
β-strand	75-76	2	13
α-helix	79-91	13
α-helix	98-100	3
β-strand	103-107	5	11
α-helix	113-125	13
β-strand	131-136	6	11
α-helix	137-144	8
β-strand	150-155	6	14
β-strand	160-166	7	14
β-strand	169-170	2	14
α-helix	172-174	3
β-strand	176-178	3	14
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	15
β-strand	247-250	4	15
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
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	14
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	14
α-helix	338-347	10
β-strand	357-358	2	11
α-helix	359-365	7
α-helix	366-368	3
α-helix	370-373	4

Chain D: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	16
β-strand	16-21	6	16
β-strand	29-32	4	16
β-strand	35-38	4	17
β-strand	41-42	2	9
β-strand	53-54	2	17
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	17
β-strand	71-72	2	18
β-strand	75-76	2	18
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	16
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	16
α-helix	137-145	9
β-strand	150-155	6	19
β-strand	160-166	7	19
β-strand	169-170	2	19
α-helix	172-174	3
β-strand	176-178	3	19
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	20
β-strand	247-250	4	20
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	19
α-helix	309-320	12
β-strand	329-330	2	19
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-354	3
β-strand	357-358	2	16
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain E: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	21
β-strand	16-21	6	21
β-strand	29-32	4	21
β-strand	35-38	4	22
β-strand	41-42	2	14
β-strand	53-54	2	22
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	22
β-strand	71-72	2	23
β-strand	75-76	2	23
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	21
α-helix	115-121	7
α-helix	122-126	5
β-strand	131-136	6	21
α-helix	137-145	9
β-strand	150-155	6	24
β-strand	160-166	7	24
β-strand	169-170	2	24
β-strand	176-178	3	24
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	25
β-strand	247-250	4	25
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-282	9
α-helix	287-289	3
α-helix	291-294	4
β-strand	297-300	4	24
α-helix	309-320	12
β-strand	329-330	2	24
α-helix	338-347	10
β-strand	357-358	2	21
α-helix	359-365	7
α-helix	369-371	3

Chain Y: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	24-25	2
α-helix	29-40	12
α-helix	43-48	6
α-helix	51-60	10
β-strand	63-65	3	26
β-strand	74-76	3	26
β-strand	81	1	27
β-strand	86-89	4	27
β-strand	94-97	4	27
β-strand	98-99	2	28
β-strand	104-105	2	28
β-strand	109-110	2	27
α-helix	118-135	18
β-strand	136	1	29
β-strand	139-146	8	30
α-helix	148-150	3
β-strand	153-164	12	30
α-helix	165-167	3
β-strand	169-180	12	30
β-strand	185-198	14	30
β-strand	203-217	15	30
α-helix	221-253	33
α-helix	255-257	3
α-helix	274-276	3
α-helix	279-281	3

Chain Z: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
α-helix	18-20	3
α-helix	21-31	11
α-helix	36-42	7
β-strand	48-52	5	31
β-strand	57-61	5	31
β-strand	66-67	2	32
β-strand	70-73	4	32
β-strand	77-80	4	32
α-helix	91-111	21
β-strand	116-123	8	30
β-strand	127-137	11	30
β-strand	145-158	14	30
β-strand	165-181	17	30
β-strand	185-201	17	30
α-helix	209-226	18
α-helix	227-232	6
α-helix	233-243	11
β-strand	244	1	29
α-helix	253-270	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	371	Oryctolagus cuniculus	P68135 (AlphaFold model)
F-actin-capping protein subunit alpha-1	Y	protein	278	Homo sapiens	P52907 (AlphaFold model)
F-actin-capping protein subunit beta	Z	protein	270	Homo sapiens	P47756 (AlphaFold model)

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

>9YIM_1 Actin, alpha skeletal muscle (chains A, B, C, D, E)
TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGI
LTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMF
ETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRD
LTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPD
GQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTT
MYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDE
AGPSIVHRKCF

Sequence of entity 2 (Y), FASTA

>9YIM_2 F-actin-capping protein subunit alpha-1 (chains Y)
VSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKI
EGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSWRESCDSA
LRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQ
VVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQTAISENY
QTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQN

Sequence of entity 3 (Z), FASTA

>9YIM_3 F-actin-capping protein subunit beta (chains Z)
SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLL
CDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYL
WDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNK
SGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVN
GLRSVQTFADKSKQEALKNDLVEALKRKQQ

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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