9M5E: Actin-related protein 3
Structure of SPIN90 dimer-Arp2/3 complex-nucleated actin filament (singlet complex). Determined by electron microscopy at 3.55 Å resolution. Released 10 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 3.55 Å
- Organisms
- Bos taurus, Homo sapiens, Gallus gallus
- Chains
- 12
- Atoms
- 29,669
- Mol. weight
- 453.89 kDa
- Ligands
- MG, ADP
- Released
- 10 Sept 2025
Explore 9M5E in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9M5E contains 222 α-helices and 155 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: 27 helices, 25 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 | 45 | 1 | 3 |
| β-strand | 48 | 1 | 3 |
| α-helix | 56-58 | 3 | |
| β-strand | 61-62 | 2 | 2 |
| α-helix | 63-66 | 4 | |
| β-strand | 72-75 | 4 | 2 |
| β-strand | 78-79 | 2 | 4 |
| β-strand | 82-83 | 2 | 4 |
| α-helix | 86-95 | 10 | |
| α-helix | 96-101 | 6 | |
| α-helix | 105-107 | 3 | |
| β-strand | 110-114 | 5 | 1 |
| α-helix | 120-127 | 8 | |
| α-helix | 128-133 | 6 | |
| β-strand | 138-143 | 6 | 1 |
| α-helix | 144-155 | 12 | |
| α-helix | 158-160 | 3 | |
| β-strand | 165-169 | 5 | 5 |
| β-strand | 175-181 | 7 | 5 |
| β-strand | 184-185 | 2 | 5 |
| α-helix | 187-189 | 3 | |
| β-strand | 191-193 | 3 | 5 |
| α-helix | 197-211 | 15 | |
| β-strand | 213 | 1 | 6 |
| β-strand | 215 | 1 | 6 |
| α-helix | 220-231 | 12 | |
| β-strand | 233 | 1 | 7 |
| α-helix | 238-247 | 10 | |
| β-strand | 254-259 | 6 | 8 |
| β-strand | 266-271 | 6 | 8 |
| α-helix | 273-275 | 3 | |
| α-helix | 279-281 | 3 | |
| α-helix | 285-287 | 3 | |
| α-helix | 296-306 | 11 | |
| α-helix | 312-317 | 6 | |
| β-strand | 319-322 | 4 | 5 |
| α-helix | 324-327 | 4 | |
| β-strand | 329 | 1 | 7 |
| α-helix | 331-352 | 22 | |
| α-helix | 362-364 | 3 | |
| β-strand | 367-368 | 2 | 5 |
| α-helix | 371-374 | 4 | |
| α-helix | 376-385 | 10 | |
| α-helix | 390-393 | 4 | |
| β-strand | 395-396 | 2 | 1 |
| α-helix | 397-402 | 6 | |
| α-helix | 405-408 | 4 | |
Chain B: 16 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8-11 | 4 | 9 |
| β-strand | 17-22 | 6 | 9 |
| β-strand | 30-33 | 4 | 9 |
| β-strand | 36-39 | 4 | 10 |
| β-strand | 40-42 | 3 | 11 |
| β-strand | 56-57 | 2 | 10 |
| α-helix | 58-63 | 6 | |
| α-helix | 65-67 | 3 | |
| β-strand | 68-71 | 4 | 10 |
| β-strand | 74-75 | 2 | 12 |
| β-strand | 78-79 | 2 | 12 |
| α-helix | 82-92 | 11 | |
| β-strand | 106-111 | 6 | 9 |
| α-helix | 117-129 | 13 | |
| β-strand | 136-140 | 5 | 9 |
| α-helix | 141-149 | 9 | |
| β-strand | 154-158 | 5 | 13 |
| β-strand | 164-170 | 7 | 13 |
| β-strand | 173-174 | 2 | 13 |
| β-strand | 180-182 | 3 | 13 |
| α-helix | 186-199 | 14 | |
| α-helix | 207-220 | 14 | |
| α-helix | 227-236 | 10 | |
| β-strand | 242-245 | 4 | 14 |
| β-strand | 251-254 | 4 | 14 |
| α-helix | 257-260 | 4 | |
| α-helix | 262-265 | 4 | |
| α-helix | 268-270 | 3 | |
| α-helix | 278-288 | 11 | |
| α-helix | 294-297 | 4 | |
| β-strand | 301-304 | 4 | 13 |
| α-helix | 306-308 | 3 | |
| α-helix | 313-328 | 16 | |
| α-helix | 334-339 | 6 | |
| β-strand | 344-345 | 2 | 13 |
Chain C: 3 helices, 31 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 15 |
| β-strand | 14-16 | 3 | 16 |
| β-strand | 22-25 | 4 | 16 |
| β-strand | 32-36 | 5 | 16 |
| β-strand | 43-48 | 6 | 16 |
| β-strand | 55-61 | 7 | 17 |
| β-strand | 66-71 | 6 | 17 |
| β-strand | 76-81 | 6 | 17 |
| β-strand | 86-87 | 2 | 17 |
| β-strand | 90 | 1 | 17 |
| β-strand | 91-92 | 2 | 18 |
| β-strand | 99-104 | 6 | 18 |
| β-strand | 111-115 | 5 | 18 |
| β-strand | 119-126 | 8 | 18 |
| β-strand | 131-137 | 7 | 18 |
| β-strand | 145-150 | 6 | 19 |
| β-strand | 156-161 | 6 | 19 |
| β-strand | 166-170 | 5 | 19 |
| α-helix | 178 | 1 | |
| α-helix | 180-182 | 3 | |
| β-strand | 194-197 | 4 | 19 |
| β-strand | 205-210 | 6 | 20 |
| β-strand | 216-221 | 6 | 20 |
| β-strand | 225-230 | 6 | 20 |
| β-strand | 236-241 | 6 | 20 |
| α-helix | 245-246 | 2 | |
| β-strand | 247-254 | 8 | 21 |
| β-strand | 257-262 | 6 | 21 |
| β-strand | 268-272 | 5 | 21 |
| β-strand | 279-281 | 3 | 21 |
| β-strand | 331-336 | 6 | 15 |
| β-strand | 341 | 1 | 21 |
| β-strand | 344-348 | 5 | 15 |
| β-strand | 354-356 | 3 | 15 |
Chain D: 19 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-23 | 15 | |
| α-helix | 26-28 | 3 | |
| β-strand | 33-35 | 3 | 22 |
| α-helix | 38-40 | 3 | |
| β-strand | 43-46 | 4 | 22 |
| α-helix | 48-50 | 3 | |
| β-strand | 54-58 | 5 | 22 |
| α-helix | 64-68 | 5 | |
| α-helix | 72-79 | 8 | |
| α-helix | 81-83 | 3 | |
| β-strand | 84-85 | 2 | 22 |
| α-helix | 87-88 | 2 | |
| β-strand | 94-98 | 5 | 22 |
| α-helix | 107-114 | 8 | |
| α-helix | 118-134 | 17 | |
| α-helix | 140-141 | 2 | |
| β-strand | 142-144 | 3 | 23 |
| β-strand | 151-156 | 6 | 23 |
| β-strand | 161-168 | 8 | 23 |
| α-helix | 172-191 | 20 | |
| α-helix | 196 | 1 | |
| β-strand | 197-201 | 5 | 23 |
| α-helix | 205-206 | 2 | |
| α-helix | 207-212 | 6 | |
| β-strand | 220-227 | 8 | 23 |
| α-helix | 229-232 | 4 | |
| α-helix | 237-244 | 8 | |
| α-helix | 247-277 | 31 | |
| α-helix | 278-280 | 3 | |
Chain E: 11 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-52 | 12 | |
| β-strand | 57-59 | 3 | 11 |
| α-helix | 63-82 | 20 | |
| α-helix | 88-99 | 12 | |
| α-helix | 103-105 | 3 | |
| α-helix | 118-120 | 3 | |
| α-helix | 123-148 | 26 | |
| β-strand | 149 | 1 | 24 |
| α-helix | 155 | 1 | |
| β-strand | 156 | 1 | 24 |
| α-helix | 157 | 1 | |
| α-helix | 158-162 | 5 | |
| α-helix | 163-165 | 3 | |
| α-helix | 168-170 | 3 | |
Chain F: 7 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-19 | 15 | |
| α-helix | 37-40 | 4 | |
| β-strand | 47 | 1 | 25 |
| α-helix | 48-50 | 3 | |
| β-strand | 51-54 | 4 | 25 |
| β-strand | 60-66 | 7 | 25 |
| β-strand | 69-75 | 7 | 25 |
| α-helix | 81-95 | 15 | |
| β-strand | 104 | 1 | 25 |
| α-helix | 108-109 | 2 | |
| β-strand | 114-119 | 6 | 25 |
| α-helix | 120-125 | 6 | |
| α-helix | 128-165 | 38 | |
Chain G: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 44-48 | 5 | |
| α-helix | 54-60 | 7 | |
| α-helix | 72-85 | 14 | |
| α-helix | 93-98 | 6 | |
| α-helix | 102-115 | 14 | |
| α-helix | 124-138 | 15 | |
| α-helix | 141-147 | 7 | |
Chain h: 28 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 312-324 | 13 | |
| α-helix | 328-345 | 18 | |
| α-helix | 347-349 | 3 | |
| α-helix | 350-361 | 12 | |
| α-helix | 377-390 | 14 | |
| α-helix | 396-400 | 5 | |
| α-helix | 407-423 | 17 | |
| α-helix | 426-433 | 8 | |
| α-helix | 439-450 | 12 | |
| α-helix | 454-470 | 17 | |
| α-helix | 472-479 | 8 | |
| α-helix | 483-493 | 11 | |
| α-helix | 498-512 | 15 | |
| α-helix | 520-522 | 3 | |
| α-helix | 523-526 | 4 | |
| α-helix | 528-540 | 13 | |
| α-helix | 550-563 | 14 | |
| α-helix | 572-579 | 8 | |
| α-helix | 585-596 | 12 | |
| α-helix | 609-611 | 3 | |
| α-helix | 613-621 | 9 | |
| α-helix | 625-628 | 4 | |
| α-helix | 633-649 | 17 | |
| α-helix | 651 | 1 | |
| α-helix | 655-670 | 16 | |
| α-helix | 680-691 | 12 | |
| α-helix | 698-713 | 16 | |
| α-helix | 715-717 | 3 | |
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 | 418 | Bos taurus | P61157 (AlphaFold model) |
| Actin-related protein 2 | B | protein | 394 | Bos taurus | A7MB62 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 1B | C | protein | 372 | Bos taurus | Q58CQ2 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 2 | D | protein | 300 | Bos taurus | Q3MHR7 (AlphaFold model) |
| Actin-related protein 2/3 complex subunit 3 | E | protein | 178 | Bos taurus | Q3T035 |
| Actin-related protein 2/3 complex subunit 4 | F | protein | 168 | Bos taurus | Q148J6 |
| Actin-related protein 2/3 complex subunit 5 | G | protein | 151 | Bos taurus | Q3SYX9 |
| NCK-interacting protein with SH3 domain | H, h | protein | 454 | Homo sapiens | Q9NZQ3 |
| Actin, alpha skeletal muscle | I, J, K | protein | 377 | Gallus gallus | P68139 |
Sequence of entity 1 (A), FASTA
>9M5E_1 Actin-related protein 3 (chains A)
MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDF
FIGDEAIEKPTYATKWPIRHGIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTP
ENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPV
AEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK
EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVV
DEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKP
KPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDYEEIGPSICRHNPVFGVMS
Sequence of entity 2 (B), FASTA
>9M5E_2 Actin-related protein 2 (chains B)
MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDE
ASELRSMLEVNYPMENGIVRNWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNR
EKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSGDGVTHICPVYEGFSLPHLTR
RLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL
VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKH
IVLSGGSTMYPGLPSRLERELKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAV
LADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR
Sequence of entity 3 (C), FASTA
>9M5E_3 Actin-related protein 2/3 complex subunit 1B (chains C)
MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGIDW
APDSNRIVTCGTDRNAYVWTLKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVI
SICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAGSCDFKCRIFSAYIKEVEERP
APTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL
ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARE
RFQNLDKKASSEGSAAAGAGLDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVR
SLESALKDLKIV
Sequence of entity 4 (D), FASTA
>9M5E_4 Actin-related protein 2/3 complex subunit 2 (chains D)
MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSIS
LKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNC
FASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDRVTVVFSTVFKDDDDVVIGKV
FMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT
INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR
Sequence of entity 5 (E), FASTA
>9M5E_5 Actin-related protein 2/3 complex subunit 3 (chains E)
MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEI
KNEADRTLIYITLYISECLKKLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKP
ANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWWTCFVKRQFMNKSLSGPGQ
Sequence of entity 6 (F), FASTA
>9M5E_6 Actin-related protein 2/3 complex subunit 4 (chains F)
MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEK
VLIEGSINSVRVSIAVKQADEIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITN
FHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIVAEEFLKNF
Sequence of entity 7 (G), FASTA
>9M5E_7 Actin-related protein 2/3 complex subunit 5 (chains G)
MSKNTVSSARFRKVDVGEYDENKFVDEEDGGDGQAGPDEGEVDSCLRQGNMTAALQAALK
NPPINTKSQAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDN
SSAVLLQWHEKALAAGGVGSIVRVLTARKTV
Sequence of entity 8 (H, h), FASTA
>9M5E_8 NCK-interacting protein with SH3 domain (chains H, h)
EPPAEEEVATGTTSASDDLEALGTLSLGTTEEKAAAEAAVPRTIGAELMELVRRNTGLSH
ELCRVAIGIIVGHIQASVPASSPVMEQVLLSLVEGKDLSMALPSGQVCHDQQRLEVIFAD
LARRKDDAQQRSWALYEDEGVIRCYLEELLHILTDADPEVCKKMCKRNEFESVLALVAYY
QMEHRASLRLLLLKCFGAMCSLDAAIISTLVSSVLPVELARDMQTDTQDHQKLCYSALIL
AMVFSMGEAVPYAHYEHLGTPFAQFLLNIVEDGLPLDTTEQLPDLCVNLLLALNLHLPAA
DQNVIMAALSKHANVKIFSEKLLLLLNRGDDPVRIFKHEPQPPHSVLKFLQDVFGSPATA
AIFYHTDMMALIDITVRHIADLSPGDKLRMEYLSLMHAIVRTTPYLQHRHRLPDLQAILR
RILNEEETSPQCQMDRMIVREMCKEFLVLGEAPS
Sequence of entity 9 (I, J, K), FASTA
>9M5E_9 Actin, alpha skeletal muscle (chains I, J, K)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 4 |
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 5 |
Primary citation
Activation of Arp2/3 complex by a SPIN90 dimer in linear actin-filament nucleation. Francis, J., Pathri, A.K., Shyam, K.T. et al. Nat Struct Mol Biol (2025) 32:2272-2284. DOI 10.1038/s41594-025-01673-8 · PubMed
Other PDB entries of the same protein (UniProt P61157 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1K8K 2.0 Å, Crystal Structure of Arp2/3 Complex
- 2P9I 2.46 Å, Crystal Structure of bovine Arp2/3 Complex co-crystallized with ADP and crosslinked with…
- 3UKR 2.48 Å, Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666
- 3ULE 2.5 Å, Structure of Bos taurus Arp2/3 complex with bound inhibitor CK-869 and ATP
- 1TYQ 2.55 Å, Crystal structure of Arp2/3 complex with bound ATP and calcium
- 1U2V 2.55 Å, Crystal structure of Arp2/3 complex with bound ADP and calcium
- 2P9K 2.59 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with ATP and crosslinked with…
- 2P9L 2.65 Å, Crystal Structure of bovine Arp2/3 complex
- 3RSE 2.65 Å, Structural and biochemical characterization of two binding sites for nucleation…
- 2P9S 2.68 Å, Structure of bovine Arp2/3 complex co-crystallized with ATP/Mg2+
- 3DXK 2.7 Å, Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636
- 2P9U 2.75 Å, Crystal structure of bovine Arp2/3 complex co-crystallized with AMP-PNP and calcium
Browse structure collections
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