6YW6: ARP2/3 1B5CL isoform complex
Cryo-EM structure of the ARP2/3 1B5CL isoform complex. Determined by electron microscopy at 4.2 Å resolution. Released 22 Jul 2020.
- Method
- Electron microscopy
- Resolution
- 4.2 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 13,823
- Mol. weight
- 225.89 kDa
- Ligands
- ATP
- Released
- 22 Jul 2020
Explore 6YW6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6YW6 contains 75 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: 23 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 1 |
| β-strand | 11-12 | 2 | 2 |
| β-strand | 16-18 | 3 | 2 |
| β-strand | 21 | 1 | 1 |
| β-strand | 30-32 | 3 | 2 |
| β-strand | 35-37 | 3 | 3 |
| β-strand | 61-62 | 2 | 3 |
| α-helix | 64-68 | 5 | |
| β-strand | 73-75 | 3 | 3 |
| β-strand | 78-79 | 2 | 4 |
| β-strand | 82-83 | 2 | 4 |
| α-helix | 86-94 | 9 | |
| β-strand | 109 | 1 | 5 |
| β-strand | 113-114 | 2 | 6 |
| α-helix | 122-132 | 11 | |
| β-strand | 138 | 1 | 5 |
| β-strand | 142-143 | 2 | 6 |
| α-helix | 144-151 | 8 | |
| α-helix | 152-154 | 3 | |
| β-strand | 165-168 | 4 | 7 |
| β-strand | 175 | 1 | 8 |
| β-strand | 177-181 | 5 | 7 |
| β-strand | 184-185 | 2 | 7 |
| β-strand | 193 | 1 | 8 |
| α-helix | 198-211 | 14 | |
| α-helix | 217-219 | 3 | |
| α-helix | 220-231 | 12 | |
| α-helix | 241-247 | 7 | |
| β-strand | 254-259 | 6 | 9 |
| β-strand | 266-271 | 6 | 9 |
| α-helix | 280-282 | 3 | |
| α-helix | 285-287 | 3 | |
| α-helix | 296-304 | 9 | |
| α-helix | 309-315 | 7 | |
| β-strand | 319-321 | 3 | 7 |
| α-helix | 324-326 | 3 | |
| α-helix | 331-346 | 16 | |
| α-helix | 348-353 | 6 | |
| α-helix | 360-362 | 3 | |
| β-strand | 367-368 | 2 | 7 |
| α-helix | 371-374 | 4 | |
| α-helix | 376-379 | 4 | |
| α-helix | 390-393 | 4 | |
| α-helix | 395-396 | 2 | |
| α-helix | 397-402 | 6 | |
| α-helix | 405-409 | 5 | |
Chain B: 13 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 19-20 | 2 | 24 |
| β-strand | 30-31 | 2 | 24 |
| α-helix | 86-89 | 4 | |
| α-helix | 141-149 | 9 | |
| β-strand | 154-159 | 6 | 25 |
| β-strand | 164-169 | 6 | 25 |
| β-strand | 174 | 1 | 25 |
| β-strand | 180-181 | 2 | 25 |
| α-helix | 187-200 | 14 | |
| α-helix | 210-220 | 11 | |
| α-helix | 231-234 | 4 | |
| β-strand | 237 | 1 | 26 |
| β-strand | 242-243 | 2 | 27 |
| β-strand | 253-254 | 2 | 27 |
| α-helix | 279-288 | 10 | |
| α-helix | 294-297 | 4 | |
| β-strand | 301-304 | 4 | 25 |
| α-helix | 306-308 | 3 | |
| α-helix | 313-324 | 12 | |
| α-helix | 325-329 | 5 | |
| α-helix | 335-338 | 4 | |
| β-strand | 344-345 | 2 | 25 |
| α-helix | 350-352 | 3 | |
| α-helix | 354-361 | 8 | |
Chain C: 2 helices, 34 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-5 | 3 | 10 |
| α-helix | 10-11 | 2 | |
| β-strand | 15-16 | 2 | 11 |
| β-strand | 22-25 | 4 | 11 |
| β-strand | 31-36 | 6 | 11 |
| β-strand | 37-38 | 2 | 12 |
| β-strand | 41-42 | 2 | 12 |
| β-strand | 46-49 | 4 | 11 |
| β-strand | 55-61 | 7 | 13 |
| β-strand | 66-71 | 6 | 13 |
| β-strand | 76-77 | 2 | 14 |
| β-strand | 78-82 | 5 | 13 |
| β-strand | 85-87 | 3 | 13 |
| β-strand | 90-91 | 2 | 14 |
| β-strand | 99-104 | 6 | 15 |
| β-strand | 110-115 | 6 | 15 |
| β-strand | 120-126 | 7 | 15 |
| β-strand | 131-137 | 7 | 15 |
| β-strand | 147 | 1 | 16 |
| β-strand | 150 | 1 | 17 |
| β-strand | 156-157 | 2 | 17 |
| β-strand | 160 | 1 | 16 |
| β-strand | 167-171 | 5 | 17 |
| β-strand | 191-197 | 7 | 17 |
| β-strand | 205-210 | 6 | 18 |
| β-strand | 216-221 | 6 | 18 |
| β-strand | 225-230 | 6 | 18 |
| β-strand | 238-241 | 4 | 18 |
| β-strand | 247-252 | 6 | 19 |
| β-strand | 257-262 | 6 | 19 |
| β-strand | 270-273 | 4 | 19 |
| β-strand | 278-281 | 4 | 19 |
| β-strand | 329-334 | 6 | 10 |
| β-strand | 344-349 | 6 | 10 |
| β-strand | 353-358 | 6 | 10 |
| α-helix | 359-362 | 4 | |
Chain D: 19 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-23 | 10 | |
| α-helix | 26-28 | 3 | |
| β-strand | 32-36 | 5 | 20 |
| α-helix | 38-40 | 3 | |
| β-strand | 42-46 | 5 | 20 |
| α-helix | 48-50 | 3 | |
| β-strand | 54-60 | 7 | 20 |
| α-helix | 64-67 | 4 | |
| α-helix | 68-70 | 3 | |
| α-helix | 73-79 | 7 | |
| α-helix | 81-83 | 3 | |
| β-strand | 84 | 1 | 20 |
| α-helix | 87-88 | 2 | |
| β-strand | 93-98 | 6 | 20 |
| α-helix | 111-113 | 3 | |
| α-helix | 118-133 | 16 | |
| α-helix | 140-142 | 3 | |
| β-strand | 143-145 | 3 | 21 |
| β-strand | 151-156 | 6 | 21 |
| β-strand | 161-166 | 6 | 21 |
| α-helix | 173-186 | 14 | |
| α-helix | 188-190 | 3 | |
| α-helix | 196-197 | 2 | |
| β-strand | 200-202 | 3 | 21 |
| α-helix | 207-209 | 3 | |
| β-strand | 221-223 | 3 | 21 |
| β-strand | 227 | 1 | 21 |
| α-helix | 229-232 | 4 | |
| α-helix | 237-244 | 8 | |
| α-helix | 247-280 | 34 | |
Chain E: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 24 | 1 | 22 |
| β-strand | 34 | 1 | 22 |
| α-helix | 41-47 | 7 | |
| α-helix | 64-81 | 18 | |
| α-helix | 88-98 | 11 | |
| α-helix | 118-120 | 3 | |
| α-helix | 123-141 | 19 | |
| α-helix | 145-148 | 4 | |
| β-strand | 149 | 1 | 23 |
| β-strand | 156 | 1 | 23 |
| α-helix | 161-163 | 3 | |
Chain F: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-19 | 15 | |
| α-helix | 37-40 | 4 | |
| β-strand | 51-54 | 4 | 28 |
| β-strand | 60-64 | 5 | 28 |
| β-strand | 70-74 | 5 | 28 |
| α-helix | 81-96 | 16 | |
| β-strand | 104 | 1 | 28 |
| β-strand | 105 | 1 | 26 |
| β-strand | 114-118 | 5 | 28 |
| α-helix | 120-124 | 5 | |
| α-helix | 128-166 | 39 | |
Chain G: 6 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 76-85 | 10 | |
| α-helix | 88-90 | 3 | |
| α-helix | 92-95 | 4 | |
| α-helix | 100-113 | 14 | |
| α-helix | 125-136 | 12 | |
| α-helix | 142-145 | 4 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Actin-related protein 3 | A | protein | 418 | Homo sapiens | P61158 (AlphaFold model) |
| ARPC1B | C | protein | 372 | Homo sapiens | O15143 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 2 | D | protein | 300 | Homo sapiens | O15144 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 3 | E | protein | 178 | Homo sapiens | O15145 (AlphaFold model) |
| Actin-related protein 2 | B | protein | 394 | Homo sapiens | P61160 |
| Actin-related protein 2/3 complex subunit 5-like protein | G | protein | 153 | Homo sapiens | Q9BPX5 |
| Actin-related protein 2/3 complex subunit 4 | F | protein | 168 | Homo sapiens | P59998 |
Sequence of entity 1 (A), FASTA
>6YW6_1 Actin-related protein 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
Sequence of entity 2 (C), FASTA
>6YW6_2 ARPC1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGAKWTKVHELKEHNGQVTGIDW
APESNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNENKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNNVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSASGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLALTFITDNSLVAAGHDCFPVLFTYDAAAGMLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGGTAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVK
SLESALKDLKIK
Sequence of entity 3 (D), FASTA
>6YW6_3 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSFLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR
Sequence of entity 4 (E), FASTA
>6YW6_4 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
Sequence of entity 5 (B), FASTA
>6YW6_5 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPAIVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR
Sequence of entity 6 (G), FASTA
>6YW6_6 Actin-related protein 2/3 complex subunit 5-like protein (chains G)
MARNTLSSRFRRVDIDEFDENKFVDEQEEAAAAAAEPGPDPSEVDGLLRQGDMLRAFHAA
LRNSPVNTKNQAVKERAQGVVLKVLTNFKSSEIEQAVQSLDRNGVDLLMKYIYKGFEKPT
ENSSAVLLQWHEKALAVGGLGSIIRVLTARKTV
Sequence of entity 7 (F), FASTA
>6YW6_7 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 2 |
Primary citation
Cryo-EM of human Arp2/3 complexes provides structural insights into actin nucleation modulation by ARPC5 isoforms. von Loeffelholz, O., Purkiss, A., Cao, L. et al. Biol Open (2020) 9. DOI 10.1242/bio.054304 · PubMed
Other PDB entries of the same protein (UniProt P61158 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9I2B 3.0 Å, SPIN90-Arp2/3 nucleated bidirectional actin filaments
- 8P94 3.3 Å, Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches
- 6UHC 3.9 Å, CryoEM structure of human Arp2/3 complex with bound NPFs
- 6YW7 4.5 Å, Cryo-EM structure of the ARP2/3 1A5C isoform complex.
Browse structure collections
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