7PDZ: Capping protein

Structure of capping protein bound to the barbed end of a cytoplasmic actin filament. Determined by electron microscopy at 3.8 Å resolution. Released 1 Sept 2021.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Mus musculus, Bos taurus, synthetic construct
Chains: 13
Atoms: 22,185
Mol. weight: 321.56 kDa
Ligands: PO4, MG, ADP
Released: 1 Sept 2021

Explore 7PDZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7PDZ contains 176 α-helices and 151 β-strands across 12 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 E: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-15	14
α-helix	18-20	3
α-helix	21-31	11
α-helix	36-42	7
β-strand	48-52	5	1
β-strand	57-61	5	1
β-strand	66-67	2	2
β-strand	70-72	3	2
β-strand	79-80	2	2
α-helix	88-90	3
α-helix	91-112	22
β-strand	116-124	9	3
β-strand	127-137	11	3
β-strand	145-158	14	3
β-strand	164-179	16	3
β-strand	186-202	17	3
α-helix	209-244	36
α-helix	247-271	25

Chain F: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-23	13
α-helix	29-39	11
α-helix	44-61	18
β-strand	64-66	3	4
β-strand	67	1	5
β-strand	73-75	3	4
β-strand	81	1	5
β-strand	86-87	2	5
β-strand	94-98	5	5
β-strand	105-110	6	5
α-helix	116-133	18
β-strand	140-148	9	3
β-strand	151-164	14	3
α-helix	165-167	3
β-strand	169-181	13	3
β-strand	185-198	14	3
β-strand	203-217	15	3
α-helix	221-241	21
α-helix	242-251	10
α-helix	252-258	7
α-helix	271-276	6

Chain I: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	6
β-strand	16-21	6	6
β-strand	29-32	4	6
β-strand	35-38	4	7
α-helix	45-47	3
β-strand	53-54	2	7
α-helix	55-60	6
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	89-94	6
α-helix	98-100	3
β-strand	103-107	5	6
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	6
α-helix	137-144	8
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	182-195	14
β-strand	198	1	10
α-helix	203-213	11
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	11
α-helix	246	1
β-strand	247-250	4	11
α-helix	253-262	10
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	302-305	4
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	9
α-helix	338-346	9
α-helix	350-355	6
β-strand	357-358	2	6
α-helix	359-365	7
α-helix	366-370	5
α-helix	371-374	4

Chain J: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
β-strand	42	1	14
α-helix	45-47	3
β-strand	54	1	13
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	13
β-strand	71-72	2	15
β-strand	75-76	2	15
α-helix	79-87	9
α-helix	88-94	7
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	150-155	6	16
β-strand	160-166	7	16
β-strand	169-170	2	16
α-helix	172-174	3
β-strand	176-178	3	16
α-helix	182-195	14
α-helix	203-216	14
α-helix	223-230	8
α-helix	234-236	3
β-strand	238-241	4	17
β-strand	247-250	4	17
α-helix	252-259	8
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	16
α-helix	302-305	4
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	16
α-helix	338-347	10
α-helix	352-354	3
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	366-368	3
α-helix	370-373	4

Chain K: 24 helices, 21 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	42	1	20
α-helix	45-47	3
β-strand	53-54	2	19
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	19
β-strand	72	1	21
β-strand	75	1	21
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	18
α-helix	113-125	13
β-strand	131-136	6	18
α-helix	137-145	9
β-strand	150-155	6	22
β-strand	160-166	7	22
β-strand	169-170	2	22
α-helix	172-174	3
β-strand	177	1	22
α-helix	182-194	13
β-strand	198	1	23
α-helix	203-215	13
α-helix	223-232	10
β-strand	238-241	4	24
β-strand	247-250	4	24
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	22
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	22
α-helix	335-337	3
α-helix	342-348	7
α-helix	350-354	5
β-strand	357-358	2	18
α-helix	359-365	7
α-helix	366-371	6

Chain L: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	25
β-strand	16-21	6	25
β-strand	29-32	4	25
β-strand	35-38	4	26
β-strand	42	1	27
α-helix	45-47	3
β-strand	53-54	2	26
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	26
β-strand	71-72	2	28
β-strand	75-76	2	28
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	25
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	25
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	182-195	14
β-strand	198	1	29
α-helix	203-214	12
α-helix	223-232	10
β-strand	238-241	4	30
β-strand	247-250	4	30
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-284	11
α-helix	288-294	7
β-strand	297-300	4	14
α-helix	302-305	4
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	14
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
α-helix	356	1
β-strand	357-358	2	25
α-helix	359-365	7
α-helix	367-371	5

Chain N: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-11	4	31
β-strand	16	1	32
β-strand	18-21	4	31
β-strand	29	1	31
β-strand	32	1	32
β-strand	35-38	4	33
α-helix	45-47	3
β-strand	53-54	2	33
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	33
β-strand	71-72	2	34
β-strand	75-76	2	34
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	31
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	31
α-helix	137-144	8
β-strand	150-155	6	20
β-strand	160-166	7	20
β-strand	169-170	2	20
α-helix	172-174	3
β-strand	176-178	3	20
α-helix	182-195	14
β-strand	198	1	35
α-helix	203-216	14
α-helix	223-233	11
β-strand	239-241	3	36
β-strand	247-249	3	36
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	20
α-helix	302-305	4
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	20
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-354	4
β-strand	357-358	2	31
α-helix	359-365	7
α-helix	366-371	6

Chain O: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	37
β-strand	16-21	6	37
β-strand	29-32	4	37
β-strand	35	1	38
β-strand	38	1	39
β-strand	54	1	38
α-helix	56-60	5
β-strand	65	1	39
β-strand	68	1	38
β-strand	71-72	2	40
β-strand	75-76	2	40
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	37
α-helix	113-125	13
β-strand	131-136	6	37
α-helix	137-143	7
β-strand	150-154	5	27
β-strand	160-166	7	27
β-strand	169-170	2	27
α-helix	172-174	3
β-strand	176-178	3	27
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-212	10
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	41
α-helix	246	1
β-strand	247-250	4	41
α-helix	252-262	11
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	27
α-helix	302-305	4
α-helix	309-320	12
α-helix	322	1
β-strand	329-330	2	27
α-helix	338-348	11
α-helix	350-354	5
β-strand	357-358	2	37
α-helix	359-365	7
α-helix	366-371	6

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
Isoform 2 of F-actin-capping protein subunit beta	E	protein	272	Mus musculus	P47757 (AlphaFold model)
F-actin-capping protein subunit alpha-1	F	protein	286	Mus musculus	P47753 (AlphaFold model)
Actin, cytoplasmic 1	I, J, K, L, N, O	protein	375	Bos taurus	P60712 (AlphaFold model)
Phalloidin	P, Q, R, S, T	protein	7	synthetic construct

Sequence of entity 1 (E), FASTA

>7PDZ_1 Isoform 2 of F-actin-capping protein subunit beta (chains E)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSVQTFADKSKQEALKNDLVEALKRKQQC

Sequence of entity 2 (F), FASTA

>7PDZ_2 F-actin-capping protein subunit alpha-1 (chains F)
MADFEDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYDDQVLITEHGDLGNSRFLDPRNQISFKFDHLRKEASDPQPEDVDGGLKSW
RESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPSAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSVTVSNEVQTTKEFIKIIESAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGKEMQNA

Sequence of entity 3 (I, J, K, L, N, O), FASTA

>7PDZ_3 Actin, cytoplasmic 1 (chains I, J, K, L, N, O)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Sequence of entity 4 (P, Q, R, S, T), FASTA

>7PDZ_4 Phalloidin (chains P, Q, R, S, T)
PAWXATC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	4
MG	Magnesium ion	Mg	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks. Funk, J., Merino, F., Schaks, M. et al. Nat Commun (2021) 12:5329-5329. DOI 10.1038/s41467-021-25682-5 · PubMed

Other PDB entries of the same protein (UniProt P47757 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P94 3.3 Å, Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches

Browse structure collections

About this viewer

MolViewer shows 7PDZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.