9M64: Actin-related protein 3

Structure of SPIN90 dimer-Arp2/3 complexes-nucleated actin filaments (Doublet Complex). Determined by electron microscopy at 3.4 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Bos taurus, Homo sapiens, Gallus gallus
Chains: 24
Atoms: 57,141
Mol. weight: 891.77 kDa
Ligands: ADP, MG
Released: 10 Sept 2025

Explore 9M64 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M64 contains 440 α-helices and 339 β-strands across 24 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: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8-12	5	47
β-strand	16-21	6	47
β-strand	29-32	4	47
β-strand	35-38	4	48
α-helix	56-58	3
β-strand	60-62	3	48
α-helix	63-65	3
β-strand	72-75	4	48
β-strand	78-79	2	49
β-strand	82-83	2	49
α-helix	86-95	10
α-helix	96-101	6
α-helix	105-107	3
β-strand	110-114	5	47
α-helix	120-128	9
α-helix	129-133	5
β-strand	138-143	6	47
α-helix	144-155	12
α-helix	156-157	2
β-strand	165-170	6	50
β-strand	175-181	7	50
β-strand	184-185	2	50
α-helix	187-189	3
β-strand	191-193	3	50
α-helix	197-209	13
α-helix	217-219	3
α-helix	220-231	12
β-strand	233	1	51
α-helix	238-247	10
α-helix	249-252	4
β-strand	254-259	6	52
β-strand	266-271	6	52
α-helix	273-275	3
α-helix	279-282	4
α-helix	285-287	3
α-helix	296-306	11
α-helix	309-316	8
β-strand	319-322	4	50
α-helix	324-327	4
β-strand	329	1	51
α-helix	331-354	24
β-strand	367-368	2	50
α-helix	376-384	9
α-helix	390-393	4
β-strand	395-396	2	47
α-helix	397-403	7
α-helix	405-408	4

Chain A: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
α-helix	40-43	4
α-helix	50-52	3
α-helix	56-58	3
β-strand	60-62	3	2
α-helix	63-65	3
β-strand	72-75	4	2
β-strand	78-79	2	3
β-strand	82-83	2	3
α-helix	86-95	10
α-helix	96-101	6
α-helix	105-107	3
β-strand	110-114	5	1
α-helix	120-128	9
α-helix	129-133	5
β-strand	138-143	6	1
α-helix	144-155	12
α-helix	157	1
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	184-185	2	4
α-helix	187-189	3
β-strand	191-193	3	4
α-helix	197-211	15
α-helix	217-231	15
β-strand	233	1	5
α-helix	238-247	10
α-helix	249-252	4
β-strand	254-259	6	6
β-strand	266-271	6	6
α-helix	273-275	3
α-helix	279-282	4
α-helix	296-304	9
α-helix	309-316	8
β-strand	319-322	4	4
α-helix	324-326	3
β-strand	329	1	5
α-helix	331-352	22
α-helix	359-362	4
β-strand	367-368	2	4
α-helix	371-374	4
α-helix	376-386	11
α-helix	388-393	6
β-strand	395-396	2	1
α-helix	397-402	6
α-helix	405-408	4

Chain b: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	53
β-strand	17-22	6	53
β-strand	31-33	3	53
β-strand	36-39	4	54
β-strand	40-42	3	55
β-strand	56-57	2	54
α-helix	58-63	6
α-helix	65-67	3
β-strand	68-71	4	54
β-strand	74-75	2	56
β-strand	78-79	2	56
α-helix	82-92	11
α-helix	102-104	3
β-strand	106-111	6	53
α-helix	117-129	13
β-strand	135-140	6	53
α-helix	141-149	9
β-strand	154-159	6	57
β-strand	164-170	7	57
β-strand	173-174	2	57
α-helix	176-178	3
β-strand	180-182	3	57
α-helix	186-197	12
α-helix	207-220	14
α-helix	227-236	10
β-strand	242-245	4	58
β-strand	251-254	4	58
α-helix	257-260	4
α-helix	262-265	4
α-helix	268-271	4
α-helix	278-286	9
α-helix	294-297	4
β-strand	301-304	4	57
α-helix	306-308	3
α-helix	313-328	16
α-helix	336-339	4
β-strand	344-345	2	57
α-helix	348-352	5
α-helix	353-364	12
β-strand	373-374	2	53

Chain B: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	7
β-strand	17-22	6	7
β-strand	30-33	4	7
β-strand	36-39	4	8
β-strand	40-42	3	9
β-strand	56-57	2	8
α-helix	58-63	6
α-helix	65-67	3
β-strand	68-71	4	8
β-strand	74-75	2	10
β-strand	78-79	2	10
α-helix	82-92	11
α-helix	102-104	3
β-strand	105-111	7	7
α-helix	117-129	13
β-strand	135-140	6	7
α-helix	141-149	9
β-strand	154-159	6	11
β-strand	164-170	7	11
β-strand	173-174	2	11
α-helix	176-178	3
β-strand	180-182	3	11
α-helix	186-199	14
α-helix	207-220	14
α-helix	227-236	10
β-strand	237	1	12
α-helix	238-240	3
β-strand	242-245	4	13
β-strand	251-254	4	13
α-helix	257-260	4
α-helix	262-265	4
α-helix	268-270	3
α-helix	278-286	9
α-helix	294-297	4
β-strand	301-304	4	11
α-helix	306-308	3
α-helix	313-328	16
α-helix	334-339	6
β-strand	344-345	2	11
α-helix	350-352	3
α-helix	353-365	13
β-strand	373-374	2	7

Chain c: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	59
α-helix	10-11	2
β-strand	14-16	3	60
β-strand	22-25	4	60
β-strand	32-38	7	60
β-strand	41-48	8	60
β-strand	55-61	7	61
β-strand	66-71	6	61
β-strand	76-82	7	61
β-strand	85-90	6	61
β-strand	91-92	2	62
β-strand	99-104	6	62
β-strand	110-115	6	62
β-strand	120-126	7	62
β-strand	131-137	7	62
β-strand	145-150	6	63
β-strand	156-161	6	63
β-strand	167-170	4	63
α-helix	178-182	5
β-strand	183	1	64
β-strand	186	1	64
β-strand	194-197	4	63
β-strand	205-210	6	65
β-strand	216-221	6	65
β-strand	225-230	6	65
α-helix	231-233	3
β-strand	236-241	6	65
β-strand	247-254	8	66
β-strand	257-262	6	66
β-strand	268-272	5	66
β-strand	279-284	6	66
β-strand	329-336	8	59
β-strand	344-349	6	59
β-strand	353-357	5	59

Chain C: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	14
β-strand	14-16	3	15
β-strand	22-25	4	15
β-strand	32-38	7	15
β-strand	41-48	8	15
β-strand	55-61	7	16
β-strand	66-71	6	16
β-strand	76-82	7	16
β-strand	85-90	6	16
β-strand	91-92	2	17
β-strand	99-104	6	17
β-strand	110-115	6	17
β-strand	120-126	7	17
β-strand	131-137	7	17
β-strand	145-150	6	18
β-strand	156-161	6	18
β-strand	167-170	4	18
α-helix	178-182	5
β-strand	193-197	5	18
β-strand	205-210	6	19
β-strand	216-221	6	19
β-strand	225-230	6	19
β-strand	236-241	6	19
β-strand	247-254	8	20
β-strand	257-262	6	20
β-strand	268-273	6	20
β-strand	278-283	6	20
β-strand	331-336	6	14
β-strand	344-348	5	14
β-strand	354-357	4	14

Chain d: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-24	16
α-helix	26-30	5
β-strand	32-36	5	67
α-helix	38-40	3
β-strand	42-46	5	67
β-strand	54-59	6	67
α-helix	64-69	6
α-helix	72-80	9
α-helix	81-83	3
α-helix	85	1
α-helix	87-88	2
β-strand	93-98	6	67
α-helix	99-101	3
α-helix	106-114	9
α-helix	116-133	18
α-helix	139-141	3
β-strand	142-144	3	68
β-strand	152-156	5	68
β-strand	161-166	6	68
α-helix	172-186	15
α-helix	187-189	3
α-helix	196	1
β-strand	197-201	5	68
α-helix	207-211	5
β-strand	222-227	6	68
α-helix	229-232	4
α-helix	237-244	8
α-helix	247-278	32

Chain D: 18 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-24	16
β-strand	32-36	5	21
α-helix	38-40	3
β-strand	42-46	5	21
α-helix	48-50	3
β-strand	54-58	5	21
α-helix	68-70	3
α-helix	74-80	7
α-helix	81-83	3
α-helix	85-88	4
β-strand	94-98	5	21
α-helix	106-114	9
α-helix	116-132	17
α-helix	139-141	3
β-strand	142-147	6	22
β-strand	150-157	8	22
β-strand	160-168	9	22
α-helix	172-186	15
α-helix	188-191	4
α-helix	196	1
β-strand	197-200	4	22
β-strand	220-227	8	22
α-helix	229-232	4
α-helix	237-244	8
α-helix	247-277	31
α-helix	278-280	3

16 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-related protein 3	A, a	protein	418	Bos taurus	P61157 (AlphaFold model)
Actin-related protein 2	B, b	protein	394	Bos taurus	A7MB62 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1B	C, c	protein	372	Bos taurus	Q58CQ2 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D, d	protein	300	Bos taurus	Q3MHR7 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E, e	protein	178	Bos taurus	Q3T035
Actin-related protein 2/3 complex subunit 4	F, f	protein	168	Bos taurus	Q148J6
Actin-related protein 2/3 complex subunit 5	G, g	protein	151	Bos taurus	Q3SYX9
NCK-interacting protein with SH3 domain	H, h	protein	454	Homo sapiens	Q9NZQ3
Actin, alpha skeletal muscle	I, J, K, L, i, j, k, l	protein	377	Gallus gallus	P68139

Sequence of entity 1 (A, a), FASTA

>9M64_1 Actin-related protein 3 (chains A, a)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Sequence of entity 2 (B, b), FASTA

>9M64_2 Actin-related protein 2 (chains B, b)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 3 (C, c), FASTA

>9M64_3 Actin-related protein 2/3 complex subunit 1B (chains C, c)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDW
APDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVR
SLESALKDLKIV

Sequence of entity 4 (D, d), FASTA

>9M64_4 Actin-related protein 2/3 complex subunit 2 (chains D, d)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E, e), FASTA

>9M64_5 Actin-related protein 2/3 complex subunit 3 (chains E, e)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 6 (F, f), FASTA

>9M64_6 Actin-related protein 2/3 complex subunit 4 (chains F, f)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G, g), FASTA

>9M64_7 Actin-related protein 2/3 complex subunit 5 (chains G, g)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H, h), FASTA

>9M64_8 NCK-interacting protein with SH3 domain (chains H, h)
EPPAEEEVATGTTSASDDLEALGTLSLGTTEEKAAAEAAVPRTIGAELMELVRRNTGLSH
ELCRVAIGIIVGHIQASVPASSPVMEQVLLSLVEGKDLSMALPSGQVCHDQQRLEVIFAD
LARRKDDAQQRSWALYEDEGVIRCYLEELLHILTDADPEVCKKMCKRNEFESVLALVAYY
QMEHRASLRLLLLKCFGAMCSLDAAIISTLVSSVLPVELARDMQTDTQDHQKLCYSALIL
AMVFSMGEAVPYAHYEHLGTPFAQFLLNIVEDGLPLDTTEQLPDLCVNLLLALNLHLPAA
DQNVIMAALSKHANVKIFSEKLLLLLNRGDDPVRIFKHEPQPPHSVLKFLQDVFGSPATA
AIFYHTDMMALIDITVRHIADLSPGDKLRMEYLSLMHAIVRTTPYLQHRHRLPDLQAILR
RILNEEETSPQCQMDRMIVREMCKEFLVLGEAPS

Sequence of entity 9 (I, J, K, L, i, j, k, l), FASTA

>9M64_9 Actin, alpha skeletal muscle (chains I, J, K, L, i, j, k, l)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	12
MG	Magnesium ion	Mg	10

Primary citation

Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation. Francis, J., Pathri, A.K., Shyam, K.T. et al. Nat Struct Mol Biol (2025) 32:2272-2284. DOI 10.1038/s41594-025-01673-8 · PubMed

Other PDB entries of the same protein (UniProt P61157 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1K8K 2.0 Å, Crystal Structure of Arp2/3 Complex
2P9I 2.46 Å, Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with…
3UKR 2.48 Å, Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666
3ULE 2.5 Å, Structure of Bos taurus Arp2/3 complex with bound inhibitor CK-869 and ATP
1TYQ 2.55 Å, Crystal structure of Arp2/3 complex with bound ATP and calcium
1U2V 2.55 Å, Crystal structure of Arp2/3 complex with bound ADP and calcium
2P9K 2.59 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with…
2P9L 2.65 Å, Crystal Structure of bovine Arp2/3 complex
3RSE 2.65 Å, Structural and biochemical characterization of two binding sites for nucleation…
2P9S 2.68 Å, Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+
3DXK 2.7 Å, Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636
2P9U 2.75 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium

Browse structure collections

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