4PKH: Actin, alpha skeletal muscle

Complex of ADP-actin With the N-terminal Actin-Binding Domain of Tropomodulin. Determined by X-ray diffraction at 2.15 Å resolution. Released 30 Jul 2014.

Method: X-ray diffraction
Resolution: 2.15 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 8
Atoms: 16,459
Mol. weight: 253.88 kDa
Ligands: CA, ADP
Released: 30 Jul 2014

Explore 4PKH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4PKH contains 122 α-helices and 110 β-strands across 8 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	22	1	2
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-37	3	3
β-strand	53-54	2	3
α-helix	56-61	6
α-helix	62-64	3
β-strand	66-68	3	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-88	10
α-helix	89-93	5
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	206-216	11
α-helix	223-233	11
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
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	338-348	11
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain B: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	57-61	5
β-strand	67-74	8	7
β-strand	77-80	4	7
α-helix	81-82	2
α-helix	83-85	3
β-strand	88	1	8
β-strand	94-102	9	7
α-helix	107	1
β-strand	108-116	9	7
α-helix	122-138	17
β-strand	144-149	6	7
α-helix	155-158	4
β-strand	166	1	8
α-helix	172-174	3
α-helix	1064-1071	8

Chain D: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	9
β-strand	16-21	6	9
β-strand	22	1	10
β-strand	24	1	10
β-strand	29-32	4	9
β-strand	35-37	3	11
β-strand	53-54	2	11
α-helix	56-59	4
β-strand	66-68	3	11
β-strand	71-72	2	12
β-strand	75-76	2	12
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	9
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	9
α-helix	137-144	8
β-strand	150-155	6	13
β-strand	160-166	7	13
β-strand	169-170	2	13
α-helix	172-174	3
β-strand	176-178	3	13
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	14
β-strand	247-250	4	14
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	13
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	13
α-helix	335-337	3
α-helix	338-346	9
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 E: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	57-60	4
β-strand	67-74	8	15
β-strand	77-80	4	15
α-helix	81-82	2
α-helix	83-85	3
β-strand	88-90	3	16
β-strand	94-102	9	15
α-helix	107	1
β-strand	108-116	9	15
α-helix	122-138	17
β-strand	144-149	6	15
α-helix	155-159	5
β-strand	166-168	3	16

Chain F: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	17
β-strand	16-21	6	17
β-strand	29-32	4	17
β-strand	35-38	4	18
α-helix	39-40	2
β-strand	53-54	2	18
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	18
β-strand	71-72	2	19
β-strand	75-76	2	19
α-helix	79-88	10
α-helix	89-94	6
β-strand	103-107	5	17
α-helix	113-125	13
β-strand	131-136	6	17
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
α-helix	206-215	10
α-helix	223-226	4
α-helix	229-231	3
β-strand	238-241	4	21
α-helix	242	1
β-strand	247-250	4	21
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	287-295	9
β-strand	297-300	4	20
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	20
α-helix	338-346	9
α-helix	353-355	3
β-strand	357-358	2	17
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain G: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	57-60	4
β-strand	67-74	8	22
β-strand	77-80	4	22
α-helix	81-82	2
α-helix	83-85	3
β-strand	88-90	3	23
β-strand	94-102	9	22
β-strand	108-116	9	22
α-helix	122-138	17
α-helix	143	1
β-strand	144-149	6	22
α-helix	155-158	4
β-strand	166-168	3	23
α-helix	1065-1071	7

Chain I: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	24
β-strand	16-21	6	24
β-strand	22	1	25
β-strand	24	1	25
β-strand	29-32	4	24
β-strand	35-37	3	26
β-strand	53-54	2	26
α-helix	55-58	4
β-strand	66-68	3	26
β-strand	71-72	2	27
β-strand	75-76	2	27
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	24
α-helix	113-125	13
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
α-helix	172-174	3
β-strand	176-178	3	28
α-helix	182-193	12
α-helix	194-196	3
α-helix	206-216	11
α-helix	223-230	8
β-strand	238-240	3	29
β-strand	248-250	3	29
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-295	9
β-strand	297-300	4	28
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	28
α-helix	338-348	11
α-helix	352-354	3
β-strand	357-358	2	24
α-helix	359-365	7
α-helix	369-373	5

Chain J: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	57-60	4
β-strand	67-73	7	30
β-strand	78-80	3	30
α-helix	81-82	2
α-helix	83-85	3
β-strand	88-90	3	31
β-strand	94-102	9	30
β-strand	108-116	9	30
α-helix	122-138	17
β-strand	143-149	7	30
α-helix	155-158	4
β-strand	166-168	3	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, D, F, I	protein	377	Oryctolagus cuniculus	P68135 (AlphaFold model)
Gelsolin,Tropomodulin-1 chimera	B, E, G, J	protein	186	Homo sapiens	P06396 (AlphaFold model), P28289 (AlphaFold model)

Sequence of entity 1 (A, D, F, I), FASTA

>4PKH_1 Actin, alpha skeletal muscle (chains A, D, F, I)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (B, E, G, J), FASTA

>4PKH_2 Gelsolin,Tropomodulin-1 chimera (chains B, E, G, J)
MVVEHPEFLKAGKEPGLQIWRVEKFDLVPVPTNLYGDFFTGDAYVILKTVQLRNGNLQYD
LHYWLGNECSQDESGAAAIFTVQLDDYLNGRAVQHREVQGFESATFLGYFKSGLKYKKGG
VASGFGGSGGSGGSQKDQTTKAPTGPFKREELLDHLEKQAKEFKDREDLVPYTGEKRGKV
WVPKQK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4

Primary citation

Actin cytoskeleton. Mechanism of actin filament pointed-end capping by tropomodulin. Rao, J.N., Madasu, Y., Dominguez, R. Science (2014) 345:463-467. DOI 10.1126/science.1256159 · 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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