8UXX: Arp2/3 branch junction complex, BeFx state

Arp2/3 branch junction complex, BeFx state. Determined by electron microscopy at 3.2 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Schizosaccharomyces pombe, Oryctolagus cuniculus
Chains: 15
Atoms: 39,062
Mol. weight: 568.74 kDa
Ligands: ADP, MG, BEF, ATP
Released: 31 Jan 2024

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

Secondary structure: helices and β-sheets

8UXX contains 289 α-helices and 262 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: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	75-76	2	2
α-helix	78-81	4
β-strand	88-91	4	2
β-strand	94-95	2	3
β-strand	98-99	2	3
α-helix	102-111	10
α-helix	112-116	5
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	160-164	5
α-helix	165-167	3
α-helix	174-176	3
β-strand	181-186	6	4
β-strand	191-197	7	4
β-strand	200-201	2	4
α-helix	203-205	3
β-strand	207-209	3	4
α-helix	213-226	14
α-helix	234-244	11
β-strand	246	1	5
α-helix	251-260	10
α-helix	262-264	3
β-strand	267-268	2	6
β-strand	271	1	7
β-strand	277	1	7
β-strand	280-281	2	6
α-helix	285-288	4
α-helix	290-292	3
α-helix	296-298	3
α-helix	307-317	11
α-helix	320-322	3
α-helix	323-328	6
β-strand	330-333	4	4
α-helix	335-337	3
β-strand	340	1	5
α-helix	342-365	24
β-strand	376-377	2	4
α-helix	382-384	3
α-helix	385-394	10
α-helix	399-402	4
β-strand	404-405	2	1
α-helix	406-412	7
α-helix	414-417	4

Chain B: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	5	1
β-strand	6-10	5	8
β-strand	14-19	6	8
β-strand	27-30	4	8
β-strand	33-36	4	9
β-strand	37-38	2	10
β-strand	53-54	2	9
α-helix	55-59	5
α-helix	62-64	3
β-strand	65-68	4	9
β-strand	71-72	2	11
β-strand	75-76	2	11
α-helix	79-88	10
α-helix	89-94	6
β-strand	102-107	6	8
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	8
α-helix	137-144	8
β-strand	152-155	4	12
β-strand	160-163	4	12
β-strand	165-166	2	13
β-strand	169-170	2	13
β-strand	176-178	3	12
α-helix	184-195	12
α-helix	205-216	12
β-strand	218	1	14
α-helix	223-232	10
β-strand	233	1	15
β-strand	238-241	4	16
β-strand	247-250	4	16
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-282	9
α-helix	290-294	5
β-strand	297-300	4	12
α-helix	302-304	3
β-strand	307	1	14
α-helix	309-324	16
α-helix	330-335	6
β-strand	340-341	2	12
α-helix	346-348	3
α-helix	349-360	12
β-strand	369-370	2	8
α-helix	371-377	7
α-helix	378-384	7

Chain C: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
β-strand	14-19	6	18
β-strand	25-30	6	18
β-strand	35-41	7	18
β-strand	44-51	8	18
β-strand	58-63	6	19
β-strand	69-74	6	19
β-strand	79-84	6	19
β-strand	90-91	2	19
β-strand	94-95	2	19
β-strand	103-108	6	20
β-strand	114-119	6	20
β-strand	124-130	7	20
β-strand	135-141	7	20
β-strand	149-154	6	21
β-strand	160-165	6	21
β-strand	169-174	6	21
α-helix	182-186	5
β-strand	187	1	22
β-strand	190	1	22
β-strand	198-203	6	21
β-strand	208-213	6	23
β-strand	220-224	5	23
β-strand	228-233	6	23
β-strand	243-248	6	23
α-helix	253	1
β-strand	254-261	8	24
β-strand	264-269	6	24
β-strand	275-280	6	24
β-strand	283-289	7	24
α-helix	292-295	4
α-helix	317-329	13
α-helix	335-339	5
β-strand	347-354	8	17
β-strand	362-367	6	17
β-strand	371-376	6	17

Chain D: 18 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	9-20	12
α-helix	24-26	3
β-strand	28-32	5	25
α-helix	34-36	3
β-strand	38-42	5	25
β-strand	49-55	7	25
α-helix	59-64	6
α-helix	67-75	9
α-helix	76-78	3
β-strand	79-80	2	25
α-helix	81-83	3
β-strand	88-93	6	25
α-helix	101-112	12
α-helix	114-118	5
α-helix	121-139	19
α-helix	144-154	11
β-strand	157-159	3	26
β-strand	165-172	8	26
β-strand	175-182	8	26
α-helix	187-203	17
α-helix	207-209	3
β-strand	214-216	3	26
α-helix	224-226	3
β-strand	239-246	8	26
α-helix	247-249	3
α-helix	255-263	9
α-helix	265-296	32
α-helix	303-306	4
β-strand	307	1	27
β-strand	313	1	27

Chain E: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
β-strand	16-17	2	28
β-strand	20-21	2	28
β-strand	25	1	29
α-helix	33-34	2
β-strand	35	1	29
α-helix	36-37	2
α-helix	43-54	12
β-strand	60-61	2	10
α-helix	65-83	19
α-helix	89-101	13
α-helix	105-106	2
α-helix	119-121	3
α-helix	124-149	26
α-helix	159-162	4
α-helix	163-166	4
α-helix	169-171	3

Chain F: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-19	14
β-strand	26	1	30
β-strand	34	1	30
α-helix	37-40	4
α-helix	44-46	3
β-strand	47-54	8	31
β-strand	60-66	7	31
β-strand	69-75	7	31
α-helix	81-96	16
β-strand	104	1	31
β-strand	105	1	15
α-helix	108-109	2
β-strand	114-119	6	31
α-helix	120-125	6
α-helix	128-165	38

Chain G: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	9-12	4
α-helix	14-16	3
α-helix	18-21	4
α-helix	23-25	3
α-helix	29-48	20
α-helix	52-59	8
α-helix	70-84	15
α-helix	92-96	5
α-helix	101-114	14
α-helix	123-137	15
α-helix	140-147	8

Chain H: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	32
β-strand	16-21	6	32
β-strand	29-32	4	32
β-strand	35-38	4	33
β-strand	43	1	4
β-strand	53-54	2	33
α-helix	56-61	6
α-helix	62-64	3
β-strand	65-68	4	33
β-strand	71-72	2	34
β-strand	75-76	2	34
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	32
α-helix	113-125	13
β-strand	131-136	6	32
α-helix	137-145	9
β-strand	150-155	6	35
β-strand	160-166	7	35
β-strand	169-170	2	35
β-strand	176-178	3	35
α-helix	182-192	11
α-helix	193-196	4
α-helix	203-216	14
α-helix	223-232	10
α-helix	234-236	3
β-strand	238-241	4	36
β-strand	247-250	4	36
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-282	9
α-helix	287-293	7
β-strand	297-298	2	37
β-strand	299-300	2	35
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	37
α-helix	335-337	3
α-helix	338-348	11
α-helix	350-352	3
β-strand	357-358	2	32
α-helix	359-363	5
α-helix	367-369	3
α-helix	370-373	4

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	377	Oryctolagus cuniculus	P68139

Sequence of entity 1 (A), FASTA

>8UXX_1 Actin-related protein 3 (chains A)
MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGS
GHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCE
PEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLT
GTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI
KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIAS
SDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHR
SEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRY
QIFGNSL

Sequence of entity 2 (B), FASTA

>8UXX_2 Actin-related protein 2 (chains B)
MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEA
VRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMC
ETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDV
AGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNY
TLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLS
GGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADI
MAQNDHMWVSKAEWEEYGVRALDKLGPRTT

Sequence of entity 3 (C), FASTA

>8UXX_3 Actin-related protein 2/3 complex subunit 1 (chains C)
MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTC
VDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSG
ARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDV
DAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP
PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFT
HTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNI
TAFTSSGTDGRVVLWTL

Sequence of entity 4 (D), FASTA

>8UXX_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYP
ELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLA
APFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVF
STKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF
VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP
DVELERKTATGRSFVRA

Sequence of entity 5 (E), FASTA

>8UXX_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF
EIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAP
PLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Sequence of entity 6 (F), FASTA

>8UXX_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQ
CLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITN
YHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Sequence of entity 7 (G), FASTA

>8UXX_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

>8UXX_8 Actin, alpha skeletal muscle (chains H, I, M, N, O, P, Q, R)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	9
MG	Magnesium ion	Mg	10
BEF	Beryllium trifluoride ion	Be F3	7
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Cryo-EM structures reveal how phosphate release from Arp3 weakens actin filament branches formed by Arp2/3 complex. Chavali, S.S., Chou, S.Z., Cao, W. et al. Nat Commun (2024) 15:2059-2059. DOI 10.1038/s41467-024-46179-x · 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
8E9B 3.5 Å, Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction
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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