6W17: Actin-related protein 3
Structure of Dip1-activated Arp2/3 complex with nucleated actin filament. Determined by electron microscopy at 3.9 Å resolution. Released 12 Aug 2020.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organisms
- Schizosaccharomyces pombe (strain 972 / ATCC 24843), Oryctolagus cuniculus, Amanita phalloides
- Chains
- 17
- Atoms
- 27,396
- Mol. weight
- 445.88 kDa
- Ligands
- MG, ATP, ADP
- Released
- 12 Aug 2020
Explore 6W17 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6W17 contains 156 α-helices and 172 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: 22 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| β-strand | 8-11 | 4 | 1 |
| β-strand | 17-21 | 5 | 1 |
| β-strand | 30-31 | 2 | 1 |
| β-strand | 35-36 | 2 | 2 |
| β-strand | 75-76 | 2 | 2 |
| α-helix | 77-82 | 6 | |
| β-strand | 91 | 1 | 2 |
| β-strand | 94-95 | 2 | 3 |
| β-strand | 98-99 | 2 | 3 |
| α-helix | 102-111 | 10 | |
| α-helix | 112-116 | 5 | |
| β-strand | 126-129 | 4 | 1 |
| α-helix | 136-144 | 9 | |
| α-helix | 145-149 | 5 | |
| β-strand | 154-158 | 5 | 1 |
| α-helix | 160-166 | 7 | |
| β-strand | 183-186 | 4 | 4 |
| β-strand | 191-194 | 4 | 4 |
| β-strand | 197 | 1 | 5 |
| β-strand | 200 | 1 | 5 |
| β-strand | 207-209 | 3 | 4 |
| α-helix | 214-227 | 14 | |
| α-helix | 235-244 | 10 | |
| α-helix | 256-260 | 5 | |
| α-helix | 262-264 | 3 | |
| β-strand | 267-269 | 3 | 6 |
| β-strand | 279-281 | 3 | 6 |
| α-helix | 285-288 | 4 | |
| α-helix | 290-292 | 3 | |
| α-helix | 307-317 | 11 | |
| α-helix | 320-322 | 3 | |
| α-helix | 323-326 | 4 | |
| β-strand | 330-331 | 2 | 7 |
| β-strand | 332-333 | 2 | 4 |
| α-helix | 335-337 | 3 | |
| α-helix | 342-365 | 24 | |
| α-helix | 371-374 | 4 | |
| β-strand | 376-377 | 2 | 7 |
| α-helix | 385-394 | 10 | |
| α-helix | 398-402 | 5 | |
| β-strand | 404-405 | 2 | 1 |
| α-helix | 406-412 | 7 | |
Chain B: 18 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-8 | 3 | 8 |
| β-strand | 14-19 | 6 | 8 |
| β-strand | 27-30 | 4 | 8 |
| α-helix | 56-58 | 3 | |
| α-helix | 79-88 | 10 | |
| α-helix | 89-93 | 5 | |
| β-strand | 103-104 | 2 | 8 |
| β-strand | 106-107 | 2 | 9 |
| α-helix | 113-125 | 13 | |
| β-strand | 135-136 | 2 | 9 |
| α-helix | 137-145 | 9 | |
| β-strand | 150-155 | 6 | 10 |
| β-strand | 160-165 | 6 | 10 |
| β-strand | 170 | 1 | 10 |
| β-strand | 176-178 | 3 | 10 |
| α-helix | 183-196 | 14 | |
| α-helix | 206-215 | 10 | |
| β-strand | 218 | 1 | 11 |
| α-helix | 223-232 | 10 | |
| β-strand | 233 | 1 | 12 |
| β-strand | 238-241 | 4 | 13 |
| β-strand | 247-250 | 4 | 13 |
| α-helix | 253-262 | 10 | |
| α-helix | 264-267 | 4 | |
| α-helix | 275-283 | 9 | |
| α-helix | 287-294 | 8 | |
| β-strand | 297-300 | 4 | 10 |
| α-helix | 302-305 | 4 | |
| β-strand | 307 | 1 | 11 |
| α-helix | 309-321 | 13 | |
| α-helix | 322-326 | 5 | |
| β-strand | 340 | 1 | 10 |
| α-helix | 346-348 | 3 | |
| α-helix | 349-361 | 13 | |
| α-helix | 378-382 | 5 | |
Chain C: 2 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 14 |
| β-strand | 19 | 1 | 15 |
| β-strand | 26-29 | 4 | 15 |
| β-strand | 35-41 | 7 | 15 |
| β-strand | 44-50 | 7 | 15 |
| β-strand | 58-64 | 7 | 16 |
| β-strand | 69-74 | 6 | 16 |
| β-strand | 78-84 | 7 | 16 |
| β-strand | 90-95 | 6 | 16 |
| β-strand | 103-108 | 6 | 17 |
| β-strand | 115-119 | 5 | 17 |
| β-strand | 124-130 | 7 | 17 |
| β-strand | 135-141 | 7 | 17 |
| β-strand | 149-153 | 5 | 18 |
| β-strand | 161-165 | 5 | 18 |
| β-strand | 169 | 1 | 19 |
| β-strand | 170-173 | 4 | 18 |
| β-strand | 187 | 1 | 20 |
| β-strand | 190 | 1 | 20 |
| β-strand | 203 | 1 | 19 |
| β-strand | 210-213 | 4 | 21 |
| β-strand | 220-223 | 4 | 21 |
| β-strand | 228-232 | 5 | 21 |
| α-helix | 240-241 | 2 | |
| β-strand | 244-248 | 5 | 21 |
| α-helix | 252-253 | 2 | |
| β-strand | 255-259 | 5 | 22 |
| β-strand | 264-268 | 5 | 22 |
| β-strand | 275-280 | 6 | 22 |
| β-strand | 283-289 | 7 | 22 |
| β-strand | 347-352 | 6 | 14 |
| β-strand | 362-367 | 6 | 14 |
| β-strand | 370-376 | 7 | 14 |
Chain D: 12 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-20 | 12 | |
| β-strand | 30-33 | 4 | 23 |
| β-strand | 37-42 | 6 | 23 |
| β-strand | 50-55 | 6 | 23 |
| α-helix | 59-65 | 7 | |
| α-helix | 68-74 | 7 | |
| β-strand | 79 | 1 | 23 |
| β-strand | 89-92 | 4 | 23 |
| α-helix | 102-112 | 11 | |
| α-helix | 114-118 | 5 | |
| α-helix | 121-138 | 18 | |
| α-helix | 144-151 | 8 | |
| β-strand | 157-159 | 3 | 24 |
| β-strand | 166-172 | 7 | 24 |
| β-strand | 175-183 | 9 | 24 |
| α-helix | 187-201 | 15 | |
| α-helix | 207-209 | 3 | |
| α-helix | 213 | 1 | |
| β-strand | 214-218 | 5 | 24 |
| α-helix | 221-223 | 3 | |
| β-strand | 238-245 | 8 | 24 |
| α-helix | 255-298 | 44 | |
Chain E: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 16-17 | 2 | 25 |
| β-strand | 20-21 | 2 | 25 |
| α-helix | 43-54 | 12 | |
| α-helix | 65-83 | 19 | |
| α-helix | 89-100 | 12 | |
| α-helix | 119-121 | 3 | |
| α-helix | 127-148 | 22 | |
| α-helix | 159-163 | 5 | |
| α-helix | 169-171 | 3 | |
Chain F: 6 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-19 | 15 | |
| β-strand | 27 | 1 | 26 |
| β-strand | 33 | 1 | 26 |
| α-helix | 37-40 | 4 | |
| α-helix | 49-50 | 2 | |
| β-strand | 51-56 | 6 | 27 |
| β-strand | 59-64 | 6 | 27 |
| β-strand | 69-75 | 7 | 27 |
| α-helix | 81-96 | 16 | |
| β-strand | 105 | 1 | 12 |
| β-strand | 114-119 | 6 | 27 |
| α-helix | 120-125 | 6 | |
| α-helix | 129-167 | 39 | |
Chain G: 7 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-49 | 15 | |
| α-helix | 52-59 | 8 | |
| α-helix | 71-85 | 15 | |
| α-helix | 92-97 | 6 | |
| α-helix | 101-115 | 15 | |
| α-helix | 124-136 | 13 | |
| α-helix | 139-146 | 8 | |
Chain H: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 236-247 | 12 | |
| α-helix | 253-265 | 13 | |
| α-helix | 276-291 | 16 | |
| α-helix | 300-308 | 9 | |
| α-helix | 326-337 | 12 | |
| α-helix | 345-358 | 14 | |
4 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 (strain 972 / ATCC 24843) | P32390 (AlphaFold model) |
| Actin-related protein 2 | B | protein | 390 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q9UUJ1 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 1 | C | protein | 377 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | P78774 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 2 | D | protein | 317 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | O14241 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 3 | E | protein | 174 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q9Y7J4 |
| Actin-related protein 2/3 complex subunit 4 | F | protein | 168 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q92352 |
| Actin-related protein 2/3 complex subunit 5 | G | protein | 152 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | Q10316 |
| Protein dip1 | H | protein | 374 | Schizosaccharomyces pombe (strain 972 / ATCC 24843) | O74771 |
| Actin, alpha skeletal muscle | I, J, K, L | protein | 377 | Oryctolagus cuniculus | P68135 |
| Phalloidin | M, N, O, P, Q | protein | 7 | Amanita phalloides | P0CU63 |
Sequence of entity 1 (A), FASTA
>6W17_1 Actin-related protein 3 (chains A)
MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGS
GHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCE
PEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLT
GTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI
KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIAS
SDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHR
SEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRY
QIFGNSL
Sequence of entity 2 (B), FASTA
>6W17_2 Actin-related protein 2 (chains B)
MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEA
VRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMC
ETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDV
AGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNY
TLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLS
GGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADI
MAQNDHMWVSKAEWEEYGVRALDKLGPRTT
Sequence of entity 3 (C), FASTA
>6W17_3 Actin-related protein 2/3 complex subunit 1 (chains C)
MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTC
VDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSG
ARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDV
DAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP
PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFT
HTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNI
TAFTSSGTDGRVVLWTL
Sequence of entity 4 (D), FASTA
>6W17_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYP
ELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLA
APFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVF
STKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF
VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP
DVELERKTATGRSFVRA
Sequence of entity 5 (E), FASTA
>6W17_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF
EIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAP
PLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL
Sequence of entity 6 (F), FASTA
>6W17_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQ
CLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITN
YHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF
Sequence of entity 7 (G), FASTA
>6W17_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLL
SYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQA
YNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL
Sequence of entity 8 (H), FASTA
>6W17_8 Protein dip1 (chains H)
MEFTDVFYNLENEKQFLAEIDELLTIPYEKNELEIGVSKFLSFINKYGEPYLITEFQLQR
CMEKFLNSPLYQLDENAVLSIFYDCFFFLKEQQTLKFIIIVFQSEIQENEYCLRLLASTG
FIPVLIKAMKQFKDRSENVAFTSFRYALFLVYYICRSRRLSPTDLVAIDEYFLVNLFKTS
EEAWNDEDMDSFGMCVLTLLSINEQFMLVRLASKGSFEIANGIMDLLSSSKVDNGIYSEG
LVFTLNREKDPRSRMLILKQLFLLFTTPATYEIFYTNDLNVLIDIFIREINNIPDELSDL
RYAYLQVLIPLLENTQVRHPPHYKTKCIVDAVNNVLISHSKSSNMEDARTTDVAIRVLEV
PWLQQEMKSLGTAQ
Sequence of entity 9 (I, J, K, L), FASTA
>6W17_9 Actin, alpha skeletal muscle (chains I, J, K, L)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF
Sequence of entity 10 (M, N, O, P, Q), FASTA
>6W17_10 Phalloidin (chains M, N, O, P, Q)
PAWXATC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 6 |
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 2 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 4 |
Primary citation
Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state. Shaaban, M., Chowdhury, S., Nolen, B.J. Nat Struct Mol Biol (2020) 27:1009-1016. DOI 10.1038/s41594-020-0481-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
- 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
- 3DWL 3.78 Å, Crystal Structure of Fission Yeast Arp2/3 Complex Lacking the Arp2 Subunit
- 6W18 4.2 Å, Structure of S. pombe Arp2/3 complex in inactive state
Browse structure collections
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