9DLX: Bovine Arp2/3 complex with N-WASP CA

Bovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1. Determined by electron microscopy at 2.91 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.91 Å
Organisms: Bos taurus, Homo sapiens
Chains: 9
Atoms: 15,551
Mol. weight: 232.12 kDa
Ligands: ATP, MG
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9DLX contains 89 α-helices and 94 β-strands across 9 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: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8-11	4	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
α-helix	39	1
β-strand	61-62	2	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
β-strand	110-113	4	1
α-helix	120-133	14
β-strand	138-142	5	1
α-helix	144-151	8
α-helix	152-154	3
β-strand	165-169	5	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	220-231	12
α-helix	238-247	10
α-helix	249-252	4
β-strand	254-259	6	5
β-strand	266-271	6	5
α-helix	274-277	4
α-helix	279-281	3
α-helix	285-287	3
α-helix	296-305	10
α-helix	309-311	3
α-helix	312-317	6
β-strand	319-322	4	4
α-helix	324-326	3
α-helix	332-354	23
α-helix	360-363	4
β-strand	367-368	2	4
α-helix	376-385	10
α-helix	388-392	5
β-strand	395-396	2	1
α-helix	397-402	6

Chain B: 20 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-13	7	6
β-strand	17-22	6	6
β-strand	30-33	4	6
β-strand	36-39	4	7
β-strand	56-57	2	7
β-strand	68-71	4	7
β-strand	74-75	2	8
β-strand	78-79	2	8
α-helix	82-92	11
α-helix	102-104	3
β-strand	105-111	7	6
α-helix	117-129	13
β-strand	135-140	6	6
α-helix	141-149	9
β-strand	154-158	5	9
β-strand	164-170	7	9
β-strand	173-174	2	9
β-strand	180-182	3	9
α-helix	186-200	15
α-helix	210-220	11
α-helix	230-236	7
β-strand	242-245	4	10
β-strand	251-254	4	10
α-helix	263-266	4
α-helix	268-271	4
α-helix	278-287	10
α-helix	291-293	3
α-helix	294-299	6
β-strand	301-304	4	9
α-helix	306-308	3
α-helix	313-325	13
α-helix	326-330	5
α-helix	335-339	5
β-strand	344-345	2	9
α-helix	350-352	3
α-helix	353-364	12
β-strand	373	1	6
α-helix	375-379	5
α-helix	382-388	7

Chain C: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	11
β-strand	5	1	12
α-helix	10-11	2
β-strand	14-16	3	13
β-strand	22-25	4	13
β-strand	32-38	7	13
β-strand	41-48	8	13
β-strand	55-60	6	14
β-strand	66-71	6	14
β-strand	76-82	7	14
β-strand	85-90	6	14
β-strand	91	1	15
β-strand	99-104	6	15
β-strand	111-115	5	15
β-strand	120-126	7	15
β-strand	131-137	7	15
β-strand	145-150	6	16
β-strand	156-161	6	16
β-strand	166-170	5	16
α-helix	177-180	4
β-strand	194-198	5	16
β-strand	207-212	6	17
β-strand	218-223	6	17
β-strand	227-232	6	17
β-strand	238-243	6	17
β-strand	249-254	6	18
β-strand	259-264	6	18
β-strand	270-274	5	18
β-strand	280-285	6	18
α-helix	288-291	4
β-strand	327-332	6	11
β-strand	342-347	6	11
β-strand	351	1	12
β-strand	352-356	5	11
α-helix	357-363	7

Chain D: 16 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
α-helix	9-24	16
α-helix	26-28	3
β-strand	33-36	4	19
α-helix	38-40	3
β-strand	42-46	5	19
α-helix	48-50	3
β-strand	54-60	7	19
α-helix	64-69	6
α-helix	72-79	8
α-helix	81-83	3
β-strand	84	1	19
α-helix	86-88	3
β-strand	93-98	6	19
α-helix	108-113	6
α-helix	116-120	5
α-helix	123-134	12
α-helix	139-141	3
β-strand	142-144	3	20
β-strand	152-156	5	20
β-strand	161-168	8	20
α-helix	172-186	15
β-strand	197-202	6	20
β-strand	220-227	8	20
α-helix	237-244	8
α-helix	247-278	32

Chain E: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	21
α-helix	33	1
β-strand	34	1	21
α-helix	35	1
α-helix	41-52	12
α-helix	64-82	19
α-helix	88-99	12
α-helix	103-105	3
β-strand	109	1	22
β-strand	111	1	22
α-helix	123-148	26
β-strand	149	1	23
β-strand	156	1	23
β-strand	168	1	24
β-strand	171	1	24

Chain F: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
α-helix	37-40	4
α-helix	44-46	3
β-strand	47	1	25
α-helix	48-50	3
β-strand	51-54	4	26
β-strand	60-65	6	26
β-strand	66	1	25
β-strand	69-75	7	26
α-helix	81-96	16
β-strand	104	1	26
α-helix	108-109	2
β-strand	114-119	6	26
α-helix	120-125	6
α-helix	128-166	39

Chain G: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	51-59	9
α-helix	69-84	16
α-helix	91-95	5
α-helix	100-113	14
α-helix	121-133	13
α-helix	139-145	7

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	466-477	12
α-helix	481-484	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-related protein 3	A	protein	412	Bos taurus	P61157 (AlphaFold model)
Actin-related protein 2	B	protein	390	Bos taurus	A7MB62 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1A	C	protein	370	Bos taurus	Q1JP79 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D	protein	285	Bos taurus	Q3MHR7 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	175	Bos taurus	Q3T035
Actin-related protein 2/3 complex subunit 4	F	protein	167	Bos taurus	Q148J6
Actin-related protein 2/3 complex subunit 5	G	protein	151	Bos taurus	Q3SYX9
Actin nucleation-promoting factor WASL	H, I	protein	41	Homo sapiens	O00401

Sequence of entity 1 (A), FASTA

>9DLX_1 Actin-related protein 3 (chains A)
GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFI
GDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPEN
REYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAE
GYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEF
NKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDE
VIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKP
IDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVF

Sequence of entity 2 (B), FASTA

>9DLX_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLG

Sequence of entity 3 (C), FASTA

>9DLX_3 Actin-related protein 2/3 complex subunit 1A (chains C)
MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGGQWVKAHELKEHNGHITGIDW
APKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLI
SVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKP
ASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVS
TLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAM
ERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTL
ESSIQGLRIM

Sequence of entity 4 (D), FASTA

>9DLX_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAE

Sequence of entity 5 (E), FASTA

>9DLX_5 Actin-related protein 2/3 complex subunit 3 (chains E)
PAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIK
NEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPA
NKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGP

Sequence of entity 6 (F), FASTA

>9DLX_6 Actin-related protein 2/3 complex subunit 4 (chains F)
TATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKV
LIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNF
HTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>9DLX_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H, I), FASTA

>9DLX_8 Actin nucleation-promoting factor WASL (chains H, I)
SGIVGALMEVMQKRSKAIHSSDEDEDEDDEEDFEDDDEWED

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
MG	Magnesium ion	Mg	2

Primary citation

NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail and conformational changes in Arp2/3 complex. Saks, A.J., Barrie, K.R., Rebowski, G. et al. Proc Natl Acad Sci U S A (2025) 122:e2421557122-e2421557122. DOI 10.1073/pnas.2421557122 · 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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