3DWL: Actin-related protein 3

Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit. Determined by X-ray diffraction at 3.78 Å resolution. Released 26 Aug 2008.

Method: X-ray diffraction
Resolution: 3.78 Å
Organism: Schizosaccharomyces pombe
Chains: 12
Atoms: 18,705
Mol. weight: 366.06 kDa
Ligands: ATP
Released: 26 Aug 2008

Explore 3DWL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DWL contains 116 α-helices and 139 β-strands across 12 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: 23 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-10	3	1
β-strand	16	1	2
β-strand	20-21	2	1
β-strand	32	1	2
β-strand	35-36	2	3
β-strand	75-76	2	3
α-helix	78-82	5
α-helix	84-87	4
β-strand	94-96	3	4
β-strand	98-99	2	4
α-helix	102-111	10
α-helix	112-116	5
α-helix	121-123	3
β-strand	125-130	6	1
α-helix	136-146	11
β-strand	154-159	6	1
α-helix	160-166	7
α-helix	167-170	4
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	213-222	10
α-helix	235-244	10
α-helix	251-257	7
β-strand	268	1	6
β-strand	281	1	6
α-helix	285-288	4
α-helix	290-293	4
α-helix	296-298	3
α-helix	307-316	10
α-helix	320-328	9
β-strand	330-333	4	5
α-helix	335-337	3
α-helix	344-354	11
β-strand	376-377	2	5
α-helix	385-395	11
α-helix	399-402	4
β-strand	404-405	2	1
α-helix	406-411	6
α-helix	414-417	4

Chain B: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	5-11	7	21
β-strand	16-21	6	21
β-strand	29-32	4	21
β-strand	35-36	2	22
β-strand	75-76	2	22
α-helix	78-82	5
α-helix	84-87	4
β-strand	94-96	3	23
β-strand	98-99	2	23
α-helix	102-111	10
α-helix	112-116	5
α-helix	121-123	3
β-strand	124-130	7	21
α-helix	136-148	13
β-strand	154-159	6	21
α-helix	160-166	7
α-helix	167-170	4
β-strand	181-186	6	24
β-strand	191-197	7	24
β-strand	200-201	2	24
α-helix	203-205	3
β-strand	208-209	2	24
α-helix	213-222	10
α-helix	235-244	10
α-helix	251-257	7
β-strand	268	1	25
β-strand	281	1	25
α-helix	285-288	4
α-helix	290-293	4
α-helix	296-298	3
α-helix	307-316	10
α-helix	320-328	9
β-strand	330-333	4	24
α-helix	335-337	3
α-helix	344-354	11
β-strand	376-377	2	24
α-helix	385-395	11
α-helix	399-402	4
β-strand	404-405	2	21
α-helix	406-411	6
α-helix	414-417	4

Chain C: 0 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	7
β-strand	18-19	2	8
β-strand	25-27	3	8
β-strand	35	1	9
β-strand	37-41	5	8
β-strand	44-47	4	8
β-strand	51	1	9
β-strand	58-63	6	10
β-strand	70-74	5	10
β-strand	79-81	3	10
β-strand	93-95	3	10
β-strand	103-107	5	11
β-strand	116-119	4	11
β-strand	124-126	3	11
β-strand	139-141	3	11
β-strand	149-154	6	12
β-strand	160-165	6	12
β-strand	170-175	6	12
β-strand	195-200	6	12
β-strand	208-213	6	13
β-strand	220-224	5	13
β-strand	228-229	2	13
β-strand	233-234	2	14
β-strand	241-243	3	14
β-strand	247-248	2	13
β-strand	254-261	8	15
β-strand	264-269	6	15
β-strand	274-277	4	15
β-strand	288	1	15
β-strand	299	1	16
β-strand	305	1	16
β-strand	347-356	10	7
β-strand	359-367	9	7
β-strand	371-375	5	7

Chains D and I: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	9-18	10
β-strand	30-33	4	17
β-strand	37-40	4	17
β-strand	52-55	4	17
α-helix	59-63	5
α-helix	67-74	8
β-strand	79-80	2	17
α-helix	81-83	3
β-strand	88-90	3	17
α-helix	104-112	9
α-helix	114-118	5
α-helix	121-127	7
α-helix	129-132	4
α-helix	149-152	4
β-strand	157-159	3	18
β-strand	167-171	5	18
β-strand	175-182	8	18
α-helix	189-201	13
α-helix	213	1
β-strand	214-217	4	18
β-strand	239-246	8	18
α-helix	247-250	4
α-helix	255-262	8
α-helix	265-297	33

Chains E and J: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	45-54	10
α-helix	68-78	11
α-helix	139-141	3
α-helix	163-166	4
α-helix	169-171	3

Chain F: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-19	15
α-helix	37-40	4
β-strand	47	1	19
β-strand	51-54	4	20
β-strand	60-65	6	20
β-strand	66	1	19
β-strand	69-75	7	20
α-helix	82-94	13
α-helix	95-97	3
β-strand	104	1	20
β-strand	114-119	6	20
α-helix	122-125	4
α-helix	128-150	23
α-helix	154-167	14

Chains G and L: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	35-38	4
α-helix	40-49	10
α-helix	53-59	7
α-helix	70-85	16
α-helix	89-91	3
α-helix	92-98	7
α-helix	101-114	14
α-helix	125-135	11
α-helix	140-145	6

Chain H: 0 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	26
β-strand	18-19	2	27
β-strand	25-27	3	27
β-strand	35	1	28
β-strand	37-41	5	27
β-strand	44-47	4	27
β-strand	51	1	28
β-strand	58-63	6	29
β-strand	70-74	5	29
β-strand	79-81	3	29
β-strand	93-95	3	29
β-strand	103-107	5	30
β-strand	116-119	4	30
β-strand	124-126	3	30
β-strand	129	1	31
β-strand	136	1	31
β-strand	139-141	3	30
β-strand	149-154	6	32
β-strand	160-165	6	32
β-strand	170-175	6	32
β-strand	195-200	6	32
β-strand	208-213	6	33
β-strand	220-224	5	33
β-strand	228-234	7	33
β-strand	241-248	8	33
β-strand	254-261	8	34
β-strand	264-269	6	34
β-strand	274-277	4	34
β-strand	288	1	34
β-strand	299	1	35
β-strand	305	1	35
β-strand	347-356	10	26
β-strand	359-367	9	26
β-strand	371-375	5	26

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, B	protein	427	Schizosaccharomyces pombe	P32390 (AlphaFold model)
Actin-related protein 2/3 complex subunit 1	C, H	protein	377	Schizosaccharomyces pombe	P78774 (AlphaFold model)
Actin-related protein 2/3 complex subunit 2	D, I	protein	317	Schizosaccharomyces pombe	O14241 (AlphaFold model)
Actin-related protein 2/3 complex subunit 3	E, J	protein	174	Schizosaccharomyces pombe	Q9Y7J4 (AlphaFold model)
Actin-related protein 2/3 complex subunit 4	F, K	protein	168	Schizosaccharomyces pombe	Q92352
Actin-related protein 2/3 complex subunit 5	G, L	protein	152	Schizosaccharomyces pombe	Q10316

Sequence of entity 1 (A, B), FASTA

>3DWL_1 Actin-related protein 3 (chains A, B)
MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGS
GHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCE
PEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLT
GTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI
KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIAS
SDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHR
SEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRY
QIFGNSL

Sequence of entity 2 (C, H), FASTA

>3DWL_2 Actin-related protein 2/3 complex subunit 1 (chains C, H)
MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTC
VDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSG
ARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDV
DAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP
PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFT
HTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNI
TAFTSSGTDGRVVLWTL

Sequence of entity 3 (D, I), FASTA

>3DWL_3 Actin-related protein 2/3 complex subunit 2 (chains D, I)
MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYP
ELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLA
APFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVF
STKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF
VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP
DVELERKTATGRSFVRA

Sequence of entity 4 (E, J), FASTA

>3DWL_4 Actin-related protein 2/3 complex subunit 3 (chains E, J)
MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF
EIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAP
PLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL

Sequence of entity 5 (F, K), FASTA

>3DWL_5 Actin-related protein 2/3 complex subunit 4 (chains F, K)
MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQ
CLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITN
YHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF

Sequence of entity 6 (G, L), FASTA

>3DWL_6 Actin-related protein 2/3 complex subunit 5 (chains G, L)
MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLL
SYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQA
YNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL

Ligands and cofactors

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

Primary citation

Structure and biochemical properties of fission yeast arp2/3 complex lacking the arp2 subunit. Nolen, B.J., Pollard, T.D. J Biol Chem (2008) 283:26490-26498. DOI 10.1074/jbc.M802607200 · 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
8E9B 3.5 Å, Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction
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

Browse structure collections

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