6W18: S. pombe Arp2/3 complex in inactive state
Structure of S. pombe Arp2/3 complex in inactive state. Determined by electron microscopy at 4.2 Å resolution. Released 12 Aug 2020.
- Method
- Electron microscopy
- Resolution
- 4.2 Å
- Organism
- Schizosaccharomyces pombe (strain 972 / ATCC 24843)
- Chains
- 7
- Atoms
- 13,151
- Mol. weight
- 227.85 kDa
- Ligands
- ATP, MG
- Released
- 12 Aug 2020
Explore 6W18 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6W18 contains 76 α-helices and 89 β-strands across 7 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: 19 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-11 | 2 | 1 |
| β-strand | 16-19 | 4 | 1 |
| β-strand | 29-32 | 4 | 1 |
| β-strand | 35-36 | 2 | 2 |
| β-strand | 75-76 | 2 | 2 |
| α-helix | 78-83 | 6 | |
| β-strand | 94-95 | 2 | 3 |
| β-strand | 98-99 | 2 | 3 |
| α-helix | 102-114 | 13 | |
| α-helix | 121-123 | 3 | |
| β-strand | 128 | 1 | 4 |
| α-helix | 136-147 | 12 | |
| β-strand | 155 | 1 | 5 |
| β-strand | 157 | 1 | 4 |
| α-helix | 160-165 | 6 | |
| α-helix | 166-170 | 5 | |
| β-strand | 181-186 | 6 | 6 |
| β-strand | 191-197 | 7 | 6 |
| β-strand | 200-201 | 2 | 6 |
| β-strand | 209 | 1 | 6 |
| α-helix | 213-222 | 10 | |
| α-helix | 235-241 | 7 | |
| α-helix | 251-259 | 9 | |
| α-helix | 285-294 | 10 | |
| α-helix | 296-299 | 4 | |
| α-helix | 307-317 | 11 | |
| α-helix | 320-326 | 7 | |
| β-strand | 331-333 | 3 | 6 |
| α-helix | 343-353 | 11 | |
| α-helix | 355-361 | 7 | |
| α-helix | 362-366 | 5 | |
| α-helix | 388-394 | 7 | |
| α-helix | 397-402 | 6 | |
| β-strand | 404 | 1 | 5 |
| α-helix | 407-410 | 4 | |
Chain B: 19 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-9 | 3 | 7 |
| β-strand | 14-18 | 5 | 7 |
| β-strand | 27-30 | 4 | 7 |
| β-strand | 33 | 1 | 8 |
| α-helix | 56-59 | 4 | |
| α-helix | 62-64 | 3 | |
| β-strand | 68 | 1 | 8 |
| β-strand | 72 | 1 | 9 |
| β-strand | 75 | 1 | 9 |
| α-helix | 79-88 | 10 | |
| α-helix | 89-93 | 5 | |
| β-strand | 105-107 | 3 | 10 |
| α-helix | 113-125 | 13 | |
| β-strand | 134-136 | 3 | 10 |
| α-helix | 137-143 | 7 | |
| β-strand | 150 | 1 | 11 |
| β-strand | 153-155 | 3 | 12 |
| β-strand | 160-162 | 3 | 12 |
| β-strand | 165-166 | 2 | 11 |
| β-strand | 169-170 | 2 | 11 |
| β-strand | 176-178 | 3 | 12 |
| α-helix | 182-195 | 14 | |
| α-helix | 208-216 | 9 | |
| α-helix | 223-232 | 10 | |
| β-strand | 238-241 | 4 | 13 |
| β-strand | 247-250 | 4 | 13 |
| α-helix | 252-254 | 3 | |
| α-helix | 259-262 | 4 | |
| α-helix | 264-267 | 4 | |
| α-helix | 274-282 | 9 | |
| α-helix | 287-293 | 7 | |
| α-helix | 294-296 | 3 | |
| β-strand | 297 | 1 | 14 |
| β-strand | 299 | 1 | 12 |
| α-helix | 302-304 | 3 | |
| α-helix | 309-322 | 14 | |
| β-strand | 340 | 1 | 14 |
| α-helix | 349-358 | 10 | |
| α-helix | 360-363 | 4 | |
Chain C: 3 helices, 33 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 27-29 | 3 | 15 |
| β-strand | 35-41 | 7 | 15 |
| β-strand | 44-51 | 8 | 15 |
| α-helix | 57 | 1 | |
| β-strand | 58-62 | 5 | 16 |
| β-strand | 70-74 | 5 | 16 |
| β-strand | 79-84 | 6 | 16 |
| β-strand | 90-94 | 5 | 16 |
| β-strand | 103-108 | 6 | 17 |
| β-strand | 114-119 | 6 | 17 |
| β-strand | 125-128 | 4 | 17 |
| α-helix | 129-130 | 2 | |
| β-strand | 149 | 1 | 18 |
| β-strand | 154 | 1 | 19 |
| β-strand | 161-162 | 2 | 19 |
| β-strand | 165 | 1 | 18 |
| β-strand | 169-170 | 2 | 20 |
| β-strand | 172-173 | 2 | 19 |
| β-strand | 202-203 | 2 | 20 |
| β-strand | 211-212 | 2 | 21 |
| β-strand | 220-223 | 4 | 21 |
| β-strand | 229-232 | 4 | 21 |
| α-helix | 240-241 | 2 | |
| β-strand | 246-247 | 2 | 21 |
| β-strand | 255 | 1 | 22 |
| β-strand | 265-267 | 3 | 23 |
| β-strand | 268 | 1 | 22 |
| β-strand | 275-277 | 3 | 23 |
| β-strand | 280 | 1 | 24 |
| β-strand | 283 | 1 | 24 |
| β-strand | 286-289 | 4 | 23 |
| β-strand | 347-352 | 6 | 25 |
| β-strand | 362 | 1 | 26 |
| β-strand | 363-367 | 5 | 25 |
| β-strand | 370-373 | 4 | 25 |
| β-strand | 376 | 1 | 26 |
Chain D: 14 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-20 | 12 | |
| β-strand | 29 | 1 | 27 |
| β-strand | 41-42 | 2 | 27 |
| β-strand | 50-52 | 3 | 27 |
| α-helix | 59-63 | 5 | |
| α-helix | 68-75 | 8 | |
| β-strand | 79 | 1 | 27 |
| β-strand | 90-92 | 3 | 27 |
| α-helix | 103-118 | 16 | |
| α-helix | 122-136 | 15 | |
| α-helix | 144-150 | 7 | |
| β-strand | 157-159 | 3 | 28 |
| β-strand | 167-171 | 5 | 28 |
| β-strand | 175-182 | 8 | 28 |
| α-helix | 187-203 | 17 | |
| α-helix | 207-209 | 3 | |
| α-helix | 213-214 | 2 | |
| β-strand | 216-218 | 3 | 28 |
| α-helix | 224-227 | 4 | |
| β-strand | 239-246 | 8 | 28 |
| α-helix | 247-250 | 4 | |
| α-helix | 252-254 | 3 | |
| α-helix | 257-262 | 6 | |
| α-helix | 265-297 | 33 | |
Chain E: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 17 | 1 | 29 |
| β-strand | 20 | 1 | 29 |
| α-helix | 43-54 | 12 | |
| α-helix | 65-83 | 19 | |
| α-helix | 89-100 | 12 | |
| α-helix | 114-117 | 4 | |
| α-helix | 127-149 | 23 | |
| β-strand | 150 | 1 | 30 |
| β-strand | 157 | 1 | 30 |
| α-helix | 159-163 | 5 | |
| α-helix | 169-171 | 3 | |
Chain F: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-19 | 15 | |
| β-strand | 51-53 | 3 | 31 |
| β-strand | 60 | 1 | 32 |
| β-strand | 61-64 | 4 | 31 |
| β-strand | 71-74 | 4 | 31 |
| β-strand | 75 | 1 | 32 |
| α-helix | 81-96 | 16 | |
| α-helix | 108-109 | 2 | |
| β-strand | 114-117 | 4 | 31 |
| α-helix | 120-125 | 6 | |
| α-helix | 128-165 | 38 | |
Chain G: 9 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-30 | 4 | |
| α-helix | 35-46 | 12 | |
| α-helix | 55-59 | 5 | |
| α-helix | 63-65 | 3 | |
| α-helix | 71-85 | 15 | |
| α-helix | 92-97 | 6 | |
| α-helix | 101-114 | 14 | |
| α-helix | 124-136 | 13 | |
| α-helix | 141-146 | 6 | |
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 |
Sequence of entity 1 (A), FASTA
>6W18_1 Actin-related protein 3 (chains A)
MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGS
GHLSSKRATEDLDFFIGNDALKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCE
PEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQAVLALAASWTSSKVTDRSLT
GTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI
KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIAS
SDFLTPLPELVDNVVQSSPIDVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHR
SEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFGSYCHTKADYEEYGASIARRY
QIFGNSL
Sequence of entity 2 (B), FASTA
>6W18_2 Actin-related protein 2 (chains B)
MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEA
VRSLLQVKYPMENGIIRDFEEMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMC
ETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVTHIVPVYESVVLNHLVGRLDV
AGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNY
TLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLS
GGSSMYAGLPSRLEKEIKQLWFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADI
MAQNDHMWVSKAEWEEYGVRALDKLGPRTT
Sequence of entity 3 (C), FASTA
>6W18_3 Actin-related protein 2/3 complex subunit 1 (chains C)
MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTC
VDWAPKSNRIVTCSQDRNAYVYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSG
ARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVLLAAGCADRKAYVLSAYVRDV
DAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP
PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFT
HTGNTGEGREEEGPVSFTALRSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNI
TAFTSSGTDGRVVLWTL
Sequence of entity 4 (D), FASTA
>6W18_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYP
ELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLA
APFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIHYRDEETIVLWPEHDRVTVVF
STKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF
VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKP
DVELERKTATGRSFVRA
Sequence of entity 5 (E), FASTA
>6W18_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNF
EIKGPADRTLIYGTLFISECLGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAP
PLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKWWTCFSKRRFMNKAL
Sequence of entity 6 (F), FASTA
>6W18_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQ
CLIESSVNSVRFSIRIKQVDEIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITN
YHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLVAETYLSCF
Sequence of entity 7 (G), FASTA
>6W18_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLL
SYVPYGNDVQEVRTQYLNAFVDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQA
YNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 2 |
| MG | Magnesium ion | Mg | 1 |
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
- 6W17 3.9 Å, Structure of Dip1-activated Arp2/3 complex with nucleated actin filament
Browse structure collections
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