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

Bovine Arp2/3 complex with N-WASP CA bound to Arp3. Determined by electron microscopy at 3.4 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Bos taurus, Homo sapiens
Chains: 9
Atoms: 15,455
Mol. weight: 231.37 kDa
Ligands: ATP, MG
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9DLZ contains 85 α-helices and 89 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, 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
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
β-strand	110-114	5	1
α-helix	120-133	14
β-strand	138-143	6	1
α-helix	144-150	7
α-helix	151-153	3
β-strand	165-169	5	4
β-strand	175-181	7	4
β-strand	184-185	2	4
β-strand	191-193	3	4
α-helix	197-211	15
α-helix	217-219	3
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	279-282	4
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	331-353	23
α-helix	360-363	4
β-strand	367-368	2	4
α-helix	376-384	9
α-helix	388-392	5
β-strand	395-396	2	1
α-helix	397-402	6

Chain B: 20 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	6	6
β-strand	17-22	6	6
β-strand	30-33	4	6
β-strand	36-37	2	7
β-strand	56-57	2	7
β-strand	71	1	7
β-strand	74-75	2	8
β-strand	78-79	2	8
α-helix	83-93	11
β-strand	106-111	6	6
α-helix	117-125	9
α-helix	126-131	6
β-strand	135-140	6	6
α-helix	141-149	9
β-strand	154-159	6	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	227-236	10
β-strand	237	1	10
β-strand	244-245	2	11
β-strand	251-252	2	11
α-helix	257-260	4
α-helix	261-265	5
α-helix	268-270	3
α-helix	278-287	10
α-helix	293-299	7
β-strand	301-304	4	9
α-helix	313-324	12
α-helix	325-329	5
α-helix	335-337	3
β-strand	344-345	2	9
α-helix	353-365	13
α-helix	369-371	3
β-strand	373	1	6
α-helix	375-381	7
α-helix	382-384	3
α-helix	385-389	5

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	12
β-strand	16	1	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	85-91	7	14
β-strand	101-104	4	15
β-strand	110-114	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	165-170	6	16
β-strand	193-199	7	16
β-strand	209-211	3	17
β-strand	218-222	5	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	288-290	3
β-strand	327-332	6	12
β-strand	342-347	6	12
β-strand	353-356	4	12
α-helix	357-363	7

Chain D: 14 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	72-80	9
β-strand	84	1	19
β-strand	93-98	6	19
α-helix	108-113	6
α-helix	116-134	19
α-helix	139-141	3
β-strand	142-144	3	20
β-strand	151-156	6	20
β-strand	161-168	8	20
α-helix	172-186	15
α-helix	188-190	3
β-strand	197-202	6	20
β-strand	220-227	8	20
α-helix	229-232	4
α-helix	234-278	45

Chain E: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	21
β-strand	19-20	2	21
β-strand	24	1	22
α-helix	33	1
β-strand	34	1	22
α-helix	41-52	12
α-helix	64-82	19
α-helix	88-99	12
α-helix	103-105	3
α-helix	123-148	26
β-strand	149-150	2	23
β-strand	155-156	2	23
α-helix	158-161	4
α-helix	168-170	3

Chain F: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
α-helix	37-40	4
β-strand	51-54	4	24
β-strand	60-65	6	24
β-strand	69-74	6	24
α-helix	75-77	3
α-helix	81-96	16
α-helix	98-101	4
β-strand	104	1	24
β-strand	105	1	10
α-helix	108-109	2
β-strand	114-119	6	24
α-helix	120-125	6
α-helix	128-166	39

Chain G: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	40-47	8
α-helix	52-58	7
α-helix	69-84	16
α-helix	91-96	6
α-helix	100-113	14
α-helix	120-131	12
α-helix	138-145	8

Chain I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	462-481	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-related protein 3	A	protein	411	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	145	Bos taurus	Q3SYX9
WASP like actin nucleation promoting factor	H, I	protein	41	Homo sapiens	A4D0Y1

Sequence of entity 1 (A), FASTA

>9DLZ_1 Actin-related protein 3 (chains A)
GRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFI
GDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPEN
REYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAE
GYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEF
NKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDE
VIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKP
IDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPV

Sequence of entity 2 (B), FASTA

>9DLZ_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLG

Sequence of entity 3 (C), FASTA

>9DLZ_3 Actin-related protein 2/3 complex subunit 1A (chains C)
MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGGQWVKAHELKEHNGHITGIDW
APKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLI
SVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKP
ASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVS
TLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAM
ERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTL
ESSIQGLRIM

Sequence of entity 4 (D), FASTA

>9DLZ_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAE

Sequence of entity 5 (E), FASTA

>9DLZ_5 Actin-related protein 2/3 complex subunit 3 (chains E)
PAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIK
NEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPA
NKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGP

Sequence of entity 6 (F), FASTA

>9DLZ_6 Actin-related protein 2/3 complex subunit 4 (chains F)
TATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKV
LIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNF
HTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>9DLZ_7 Actin-related protein 2/3 complex subunit 5 (chains G)
SSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINT
KSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLL
QWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H, I), FASTA

>9DLZ_8 WASP like actin nucleation promoting factor (chains H, I)
SGIVGALMEVMQKRSKAIHSSDEDEDEEEEEDFEDDDEWED

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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