7T5Q: Transition State of Arp2/3 Complex Activation

Cryo-EM Structure of a Transition State of Arp2/3 Complex Activation. Determined by electron microscopy at 3.4 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Bos taurus, Oryctolagus cuniculus, Homo sapiens
Chains: 10
Atoms: 21,671
Mol. weight: 345.23 kDa
Ligands: MG, ATP, ADP
Released: 14 Jun 2023

Explore 7T5Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7T5Q contains 114 α-helices and 131 β-strands across 10 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: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-37	3	2
α-helix	56-58	3
β-strand	61-62	2	2
α-helix	63-66	4
β-strand	73-75	3	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	109-113	5	1
α-helix	120-134	15
β-strand	138-142	5	1
α-helix	144-150	7
α-helix	151-155	5
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	197-208	12
α-helix	220-230	11
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	279-282	4
α-helix	285-287	3
α-helix	296-304	9
α-helix	309-311	3
α-helix	312-317	6
β-strand	319-322	4	4
α-helix	324-326	3
β-strand	329	1	5
α-helix	331-353	23
α-helix	360-364	5
β-strand	367-368	2	4
α-helix	376-385	10
α-helix	388-392	5
β-strand	395-396	2	1

Chain B: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	7
β-strand	17-22	6	7
β-strand	30-33	4	7
β-strand	36-38	3	8
β-strand	56-57	2	8
α-helix	60-63	4
β-strand	69-71	3	8
β-strand	74-75	2	9
β-strand	78-79	2	9
α-helix	85-92	8
β-strand	106-111	6	7
α-helix	117-130	14
β-strand	135-140	6	7
α-helix	141-147	7
β-strand	154-158	5	10
β-strand	164-169	6	10
β-strand	174	1	10
α-helix	176-178	3
β-strand	180-182	3	10
α-helix	186-198	13
α-helix	210-219	10
α-helix	227-236	10
β-strand	242-245	4	11
β-strand	251-254	4	11
α-helix	256-259	4
α-helix	261-264	4
α-helix	268-271	4
α-helix	277-286	10
α-helix	291-293	3
α-helix	294-298	5
β-strand	301-304	4	10
α-helix	306-308	3
α-helix	313-324	12
β-strand	344-345	2	10
α-helix	353-364	12
β-strand	373-374	2	7
α-helix	375-380	6

Chain C: 2 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	12
β-strand	14-16	3	13
β-strand	23-25	3	13
β-strand	32-37	6	13
β-strand	42-48	7	13
β-strand	55-61	7	14
β-strand	66-71	6	14
β-strand	76-81	6	14
β-strand	86-90	5	14
β-strand	91	1	15
β-strand	99-104	6	15
β-strand	110-115	6	15
β-strand	119-126	8	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
α-helix	177-180	4
β-strand	183	1	17
β-strand	186	1	17
β-strand	194-198	5	16
β-strand	207-212	6	18
β-strand	218-223	6	18
β-strand	227-232	6	18
β-strand	238-243	6	18
β-strand	249-254	6	19
β-strand	259-264	6	19
β-strand	270-274	5	19
β-strand	280-285	6	19
β-strand	327-332	6	12
α-helix	336-338	3
β-strand	342-347	6	12
β-strand	351-356	6	12

Chain D: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	26-28	3
β-strand	33-34	2	20
α-helix	38-40	3
β-strand	43-46	4	20
β-strand	54-59	6	20
α-helix	64-69	6
α-helix	72-80	9
α-helix	81-83	3
β-strand	84	1	20
α-helix	86-88	3
β-strand	93-98	6	20
α-helix	106-113	8
α-helix	116-134	19
β-strand	142-144	3	21
β-strand	152-156	5	21
β-strand	161-168	8	21
α-helix	172-182	11
α-helix	185-191	7
β-strand	197-202	6	21
α-helix	207-210	4
β-strand	220-227	8	21
α-helix	237-244	8
α-helix	248-278	31

Chain E: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-47	7
α-helix	49-52	4
α-helix	65-81	17
α-helix	88-98	11
α-helix	103-105	3
α-helix	114-116	3
α-helix	125-148	24
β-strand	149	1	22
β-strand	156	1	22
α-helix	168-170	3

Chain F: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	5-17	13
α-helix	44-46	3
β-strand	51-56	6	23
β-strand	59-64	6	23
β-strand	69-74	6	23
α-helix	81-96	16
β-strand	104	1	23
α-helix	108-109	2
β-strand	114-119	6	23
α-helix	120-124	5
α-helix	129-167	39

Chain G: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	80-85	6
α-helix	102-113	12
α-helix	121-136	16
α-helix	138-145	8

Chain H: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	7	1
β-strand	8-11	4	24
β-strand	16-20	5	24
β-strand	29-32	4	24
β-strand	35-36	2	25
β-strand	53-54	2	25
α-helix	56-60	5
β-strand	68	1	25
β-strand	71-72	2	26
β-strand	75-76	2	26
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-105	3	24
β-strand	106-107	2	27
α-helix	113-124	12
β-strand	131-132	2	28
β-strand	135-136	2	27
α-helix	138-145	8
β-strand	150-153	4	29
β-strand	160-166	7	29
β-strand	169-170	2	29
β-strand	176-178	3	29
α-helix	182-196	15
α-helix	203-205	3
α-helix	206-215	10
α-helix	223-232	10
β-strand	238-241	4	30
β-strand	247-250	4	30
α-helix	252-254	3
α-helix	258-261	4
α-helix	277-283	7
α-helix	290-294	5
β-strand	297-298	2	29
α-helix	309-318	10
β-strand	329-330	2	29
α-helix	335-337	3
α-helix	338-347	10
α-helix	350-353	4
β-strand	357-358	2	28
α-helix	359-365	7
α-helix	369-371	3

2 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	418	Bos taurus	P61157 (AlphaFold model)
Actin-related protein 2	B	protein	394	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	300	Bos taurus	Q3MHR7 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	178	Bos taurus	Q3T035
Actin-related protein 2/3 complex subunit 4	F	protein	168	Bos taurus	Q148J6
Actin-related protein 2/3 complex subunit 5	G	protein	151	Bos taurus	Q3SYX9
Actin, alpha skeletal muscle	H	protein	375	Oryctolagus cuniculus	P68135
F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera	I	protein	346	Homo sapiens, Mus musculus	P52907, Q91YD9
F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera	J	protein	333	Homo sapiens, Mus musculus	P47756, Q91YD9

Sequence of entity 1 (A), FASTA

>7T5Q_1 Actin-related protein 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS

Sequence of entity 2 (B), FASTA

>7T5Q_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR

Sequence of entity 3 (C), FASTA

>7T5Q_3 Actin-related protein 2/3 complex subunit 1A (chains C)
MSLHQFLLEPITCHAWNRDRTQIALSPNNHEVHIYKKNGGQWVKAHELKEHNGHITGIDW
APKSDRIVTCGADRNAYVWSQKDGVWKPTLVILRINRAATFVKWSPLENKFAVGSGARLI
SVCYFESENDWWVSKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRVFSAYIKEVDEKP
ASTPWGSKMPFGQLMSEFGGSGTGGWVHGVSFSASGSRLAWVSHDSTVSVADASKSVQVS
TLKTEFLPLLSVSFVSENSVVAAGHDCCPMLFNYDDRGCLTFVSKLDIPKQSIQRNMSAM
ERFRNMDKRATTEDRNTALETLHQNSITQVSIYEVDKQDCRKFCTTGIDGAMTIWDFKTL
ESSIQGLRIM

Sequence of entity 4 (D), FASTA

>7T5Q_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR

Sequence of entity 5 (E), FASTA

>7T5Q_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ

Sequence of entity 6 (F), FASTA

>7T5Q_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF

Sequence of entity 7 (G), FASTA

>7T5Q_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV

Sequence of entity 8 (H), FASTA

>7T5Q_8 Actin, alpha skeletal muscle (chains H)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 9 (I), FASTA

>7T5Q_9 F-actin-capping protein subunit alpha-1/Actin nucleation-promoting factor WASL chimera (chains I)
MADFDDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMD
QFTPVKIEGYEDQVLITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEADGGLKSW
RESCDSALRAYVKDHYSNGFCTVYAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFT
ITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQDSLTVSNEAQTAKEFIKIIENAENEYQ
TAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILSYKIGQIRQGIQLKSVSDGQESTPP
TPAPTSGIVGALMEVMQKRSKAIHSSDEDEDDDDEEDFEDDDEWED

Sequence of entity 10 (J), FASTA

>7T5Q_10 F-actin-capping protein subunit beta/Actin nucleation-promoting factor WASL chimera (chains J)
MSDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYL
LCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVY
LWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTN
KSGSGTMNLGGSLTRQMEKDETVSDCSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIV
NGLRSIDAIPDNQKFKQLQRELSQVLTQRQIGIQLKSVSDGQESTPPTPAPTSGIVGALM
EVMQKRSKAIHSSDEDEDDDDEEDFEDDDEWED

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Transition State of Arp2/3 Complex Activation by Actin-Bound Dimeric Nucleation-Promoting Factor. van Eeuwen, T., Boczkowska, M., Rebowski, G. et al. Proc Natl Acad Sci U S A (2023) 120:e2306165120-e2306165120. DOI 10.1073/pnas.2306165120 · 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

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