8E9B: S. pombe Arp2/3 complex in the branch junction

Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction. Determined by electron microscopy at 3.5 Å resolution. Released 1 Feb 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Schizosaccharomyces pombe, Gallus gallus
Chains: 15
Atoms: 39,160
Mol. weight: 566.41 kDa
Ligands: MG, ADP, ATP
Released: 1 Feb 2023

Explore 8E9B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E9B contains 278 α-helices and 261 β-strands across 15 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
α-helix	4-7	4
β-strand	8-9	2	1
β-strand	12	1	2
β-strand	16-19	4	2
β-strand	21	1	1
β-strand	29-32	4	2
β-strand	35-37	3	3
β-strand	74-76	3	3
α-helix	77-82	6
β-strand	89-91	3	3
β-strand	94-95	2	4
β-strand	98-99	2	4
α-helix	102-111	10
α-helix	112-117	6
α-helix	121-123	3
β-strand	125-130	6	1
α-helix	136-144	9
α-helix	145-150	6
β-strand	154-159	6	1
α-helix	163-168	6
β-strand	181-186	6	5
β-strand	191-197	7	5
β-strand	200-201	2	5
α-helix	203-205	3
β-strand	207-209	3	5
α-helix	213-226	14
α-helix	234-243	10
α-helix	251-260	10
β-strand	267-269	3	6
β-strand	279-281	3	6
α-helix	285-288	4
α-helix	291-294	4
α-helix	307-317	11
α-helix	320-322	3
α-helix	323-328	6
β-strand	330-333	4	5
α-helix	335-337	3
α-helix	342-365	24
β-strand	376-377	2	5
α-helix	385-394	10
α-helix	399-402	4
β-strand	404-405	2	1
α-helix	406-412	7

Chain B: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	4-5	2
β-strand	6-10	5	7
β-strand	14-19	6	7
β-strand	27-30	4	7
β-strand	33-36	4	8
β-strand	37-39	3	9
β-strand	53-54	2	8
α-helix	56-61	6
α-helix	62-64	3
β-strand	65-68	4	8
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-88	10
α-helix	89-93	5
β-strand	102-107	6	7
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	7
α-helix	137-144	8
β-strand	150-155	6	11
β-strand	160-165	6	11
β-strand	170	1	11
α-helix	172-174	3
β-strand	178	1	11
α-helix	182-196	15
α-helix	204-215	12
α-helix	223-232	10
β-strand	233	1	12
β-strand	238-241	4	13
β-strand	247-250	4	13
α-helix	253-256	4
α-helix	259-262	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	11
α-helix	302-305	4
α-helix	309-324	16
α-helix	333-335	3
β-strand	340-341	2	11
α-helix	349-360	12
α-helix	365-367	3
β-strand	369	1	7
α-helix	371-376	6
α-helix	379-381	3

Chain C: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	14
β-strand	17-19	3	15
β-strand	25-29	5	15
β-strand	35-41	7	15
β-strand	44-51	8	15
β-strand	58-64	7	16
β-strand	69-74	6	16
β-strand	79-84	6	16
β-strand	90-91	2	16
β-strand	94-95	2	16
β-strand	103-108	6	17
β-strand	114-119	6	17
β-strand	125-130	6	17
β-strand	135-140	6	17
β-strand	149-154	6	18
β-strand	160-165	6	18
β-strand	169-174	6	18
α-helix	183-186	4
β-strand	198-203	6	18
β-strand	210-213	4	19
β-strand	220-223	4	19
β-strand	228-233	6	19
β-strand	236	1	20
β-strand	239	1	20
β-strand	243-248	6	19
α-helix	253	1
β-strand	254-261	8	21
β-strand	264-269	6	21
β-strand	274-280	7	21
β-strand	283-289	7	21
α-helix	314-316	3
α-helix	317-329	13
β-strand	347-354	8	14
β-strand	362-367	6	14
β-strand	371-376	6	14

Chain D: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
β-strand	28-32	5	22
α-helix	34-36	3
β-strand	38-42	5	22
β-strand	49-55	7	22
α-helix	59-64	6
α-helix	68-75	8
α-helix	76-78	3
β-strand	79-80	2	22
α-helix	81-83	3
β-strand	88-93	6	22
α-helix	94-96	3
α-helix	101-112	12
α-helix	114-119	6
α-helix	121-139	19
α-helix	141-143	3
α-helix	144-154	11
β-strand	157-162	6	23
β-strand	165-171	7	23
β-strand	176-180	5	23
α-helix	188-205	18
α-helix	207-209	3
α-helix	213	1
β-strand	214-217	4	23
α-helix	224-226	3
β-strand	241-245	5	23
α-helix	247-250	4
α-helix	255-295	41

Chain E: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16-17	2	24
β-strand	20-21	2	24
α-helix	33-37	5
α-helix	43-54	12
β-strand	59-61	3	9
α-helix	65-83	19
α-helix	90-100	11
α-helix	119-121	3
α-helix	124-149	26
α-helix	159-162	4
α-helix	169-171	3

Chain F: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
α-helix	37-40	4
α-helix	44-46	3
α-helix	48-50	3
β-strand	51-56	6	25
β-strand	59-64	6	25
β-strand	70-74	5	25
α-helix	81-96	16
α-helix	98-100	3
β-strand	104	1	25
β-strand	105	1	12
α-helix	108-109	2
β-strand	114-118	5	25
α-helix	120-125	6
α-helix	131-166	36

Chain G: 11 helices, 0 β-strands

Element	Residues	Length
α-helix	9-12	4
α-helix	18-20	3
α-helix	23-24	2
α-helix	29-48	20
α-helix	52-60	9
α-helix	70-85	16
α-helix	89-91	3
α-helix	92-97	6
α-helix	101-115	15
α-helix	123-136	14
α-helix	140-146	7

Chain H: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	70
β-strand	16-21	6	70
β-strand	29-32	4	70
β-strand	35-38	4	71
β-strand	53-54	2	71
α-helix	56-60	5
β-strand	65-68	4	71
β-strand	71-72	2	72
β-strand	75-76	2	72
α-helix	79-88	10
α-helix	89-94	6
β-strand	105-107	3	70
α-helix	113-127	15
β-strand	131-132	2	73
β-strand	134-136	3	70
α-helix	137-144	8
β-strand	150-155	6	74
β-strand	160-165	6	74
β-strand	170	1	74
α-helix	172-174	3
β-strand	176-178	3	74
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-215	13
α-helix	223-229	7
β-strand	238-241	4	75
β-strand	247-250	4	75
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-284	11
α-helix	287-293	7
β-strand	297-300	4	74
α-helix	303-305	3
α-helix	309-320	12
β-strand	330	1	74
α-helix	338-348	11
α-helix	350-355	6
β-strand	357-358	2	73
α-helix	359-365	7
α-helix	369-373	5

7 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	427	Schizosaccharomyces pombe	P32390 (AlphaFold model)
Actin-related protein 2	B	protein	390	Schizosaccharomyces pombe	Q9UUJ1 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1	C	protein	377	Schizosaccharomyces pombe	P78774 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D	protein	317	Schizosaccharomyces pombe	O14241 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E	protein	174	Schizosaccharomyces pombe	Q9Y7J4
Actin-related protein 2/3 complex subunit 4	F	protein	168	Schizosaccharomyces pombe	Q92352
Actin-related protein 2/3 complex subunit 5	G	protein	152	Schizosaccharomyces pombe	Q10316
Actin, alpha skeletal muscle	H, I, M, N, O, P, Q, R	protein	375	Gallus gallus	P68139

Sequence of entity 1 (A), FASTA

>8E9B_1 Actin-related protein 3 (chains A)
MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGS
GHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCE
PEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLT
GTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI
KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIAS
SDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHR
SEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRY
QIFGNSL

Sequence of entity 2 (B), FASTA

>8E9B_2 Actin-related protein 2 (chains B)
MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEA
VRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMC
ETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDV
AGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNY
TLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLS
GGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADI
MAQNDHMWVSKAEWEEYGVRALDKLGPRTT

Sequence of entity 3 (C), FASTA

>8E9B_3 Actin-related protein 2/3 complex subunit 1 (chains C)
MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTC
VDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSG
ARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDV
DAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP
PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFT
HTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNI
TAFTSSGTDGRVVLWTL

Sequence of entity 4 (D), FASTA

>8E9B_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYP
ELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLA
APFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVF
STKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF
VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP
DVELERKTATGRSFVRA

Sequence of entity 5 (E), FASTA

>8E9B_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF
EIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAP
PLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Sequence of entity 6 (F), FASTA

>8E9B_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQ
CLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITN
YHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Sequence of entity 7 (G), FASTA

>8E9B_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLL
SYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQA
YNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL

Sequence of entity 8 (H, I, M, N, O, P, Q, R), FASTA

>8E9B_8 Actin, alpha skeletal muscle (chains H, I, M, N, O, P, Q, R)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	10
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	9
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Mechanism of actin filament branch formation by Arp2/3 complex revealed by a high-resolution cryo-EM structureof the branch junction. Chou, S.Z., Chatterjee, M., Pollard, T.D. Proc Natl Acad Sci U S A (2022) 119:e2206722119-e2206722119. DOI 10.1073/pnas.2206722119 · PubMed

Other PDB entries of the same protein (UniProt P32390 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8UXW 2.7 Å, Arp2/3 branch junction complex, ADP state
8UXX 3.2 Å, Arp2/3 branch junction complex, BeFx state
3DWL 3.78 Å, Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit
6W17 3.9 Å, Structure of Dip1-activated Arp2/3 complex with nucleated actin filament
6W18 4.2 Å, Structure of S. pombe Arp2/3 complex in inactive state

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