Arp2/3 branch junction complex, BeFx state

2026-08-12 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update STRUCTURE_SUMMARY entity entity_src_nat struct_ref struct_ref_seq _entity.pdbx_ec _entity_src_nat.common_name _entity_src_nat.pdbx_ncbi_taxonomy_id _entity_src_nat.pdbx_organism_scientific _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref_seq.pdbx_db_accession REMEDIATION REPOSITORY Metalloprotein remediation STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_struct_conn_angle pdbx_validate_close_contact struct_conn _em_admin.last_update _pdbx_entry_details.has_protein_modification RCSB RCSB 2023-11-11 2024-01-31 2024-01-31 2026-08-12 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R35GM136656 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM026338 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM110530 United States Arp2/3 branch junction complex, BeFx state Chavali SS Chou SZ Sindelar CV actin, arp2/3, cytoskeleton, branch, CYTOSOLIC PROTEIN Chavali SS Chou SZ Cao W Pollard TD De La Cruz EM Sindelar CV Cryo-EM structures reveal how phosphate release from Arp3 weakens actin filament branches formed by Arp2/3 complex. Nat Commun UK 15 2059 2059 2024 38448439 doi:10.1038/s41467-024-46179-x 2041-1723 EMD-42787 other EM volume

Arp2/3 branch junction complex, ADP state

8uxx FULLOVERLAP EMDB EMD-42788 associated EM volume

EMDB EMD-42787 other EM volume

Arp2/3 branch junction complex, ADP state

Arp2/3 branch complex (ADP-BeFx state) Arp2/3 branch complex (ADP-BeFx state) 0 1 2 3 4 5 6 7 8

S. pombe arp2/3 complex (ADP-Befx state) in a branch junction with chicken skeletal actin mother and daughter filaments (ADP-BeFx state)

Arp2/3 complex 1 1 2 3 4 5 6 7

S. pombe arp2/3 complex (ADP state)

Schizosaccharomyces pombe Actin 1 8

Actin mother and daughter filaments

Gallus gallus Actin-related protein 3 Schizosaccharomyces pombe 0.047427137 1 LEVO MASFNVPIIMDNGTGYSKLGYAGNDAPSYVFPTVIATRSAGASSGPAVSSKPSYMASKGSGHLSSKRATEDLDFFIGNDA LKKASAGYSLDYPIRHGQIENWDHMERFWQQSLFKYLRCEPEDHYFLLTEPPLNPPENRENTAEIMFESFNCAGLYIAVQ AVLALAASWTSSKVTDRSLTGTVVDSGDGVTHIIPVAEGYVIGSSIKTMPLAGRDVTYFVQSLLRDRNEPDSSLKTAERI KEECCYVCPDIVKEFSRFDREPDRYLKYASESITGHSTTIDVGFERFLAPEIFFNPEIASSDFLTPLPELVDNVVQSSPI DVRKGLYKNIVLSGGSTLFKNFGNRLQRDLKRIVDERIHRSEMLSGAKSGGVDVNVISHKRQRNAVWFGGSLLAQTPEFG SYCHTKADYEEYGASIARRYQIFGNSL P32390 Actin-related protein 2 Schizosaccharomyces pombe 0.044286758 1 LEVO MESAPIVLDNGTGFVKVGYAKDNFPRFQFPSIVGRPILRAEEKTGNVQIKDVMVGDEAEAVRSLLQVKYPMENGIIRDFE EMNQLWDYTFFEKLKIDPRGRKILLTEPPMNPVANREKMCETMFERYGFGGVYVAIQAVLSLYAQGLSSGVVVDSGDGVT HIVPVYESVVLNHLVGRLDVAGRDATRYLISLLLRKGYAFNRTADFETVREMKEKLCYVSYDLELDHKLSEETTVLMRNY TLPDGRVIKVGSERYECPECLFQPHLVGSEQPGLSEFIFDTIQAADVDIRKYLYRAIVLSGGSSMYAGLPSRLEKEIKQL WFERVLHGDPARLPNFKVKIEDAPRRRHAVFIGGAVLADIMAQNDHMWVSKAEWEEYGVRALDKLGPRTT Q9UUJ1 Actin-related protein 2/3 complex subunit 1 Schizosaccharomyces pombe 0.041643465 1 LEVO MATSQVLHILPKPSYEHAFNSQRTEFVTTTATNQVELYEQDGNGWKHARTFSDHDKIVTCVDWAPKSNRIVTCSQDRNAY VYEKRPDGTWKQTLVLLRLNRAATFVRWSPNEDKFAVGSGARVISVCYFEQENDWWVSKHLKRPLRSTILSLDWHPNNVL LAAGCADRKAYVLSAYVRDVDAKPEASVWGSRLPFNTVCAEYPSGGWVHAVGFSPSGNALAYAGHDSSVTIAYPSAPEQP PRALITVKLSQLPLRSLLWANESAIVAAGYNYSPILLQGNESGWAHTRDLDAGTSKTSFTHTGNTGEGREEEGPVSFTAL RSTFRNMDLKGSSQSISSLPTVHQNMIATLRPYAGTPGNITAFTSSGTDGRVVLWTL P78774 Actin-related protein 2/3 complex subunit 2 Schizosaccharomyces pombe 0.03702523 1 LEVO MLSLDYNNIFIYELLTERFSSENPSSIDQVVTDFDGVTFHISTPEEKTKILISLSMKCYPELVNYGTLDLLKQIYGAYVH EPEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVLAAPFHRAFTKQAELADLARKDPENAPMLDKQATSQELMAIH YRDEETIVLWPEHDRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQKGDDFGF VTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQKVLNRAKPDVELERKTATGRSFVRA O14241 Actin-related protein 2/3 complex subunit 3 Schizosaccharomyces pombe 0.019865745999999997 1 LEVO MPAYHSSFLSLTDVPTTGNIAMLPLKTKFRGPAYPADESQMDIIDECIGLFRANCFFRNFEIKGPADRTLIYGTLFISEC LGRVNGLNYRDAERQLNSLALENFSIPGSAGFPLNALYAPPLSPQDAEIMRTYLTQFRQELAYRLLSHVYATEKDHPSKW WTCFSKRRFMNKAL Q9Y7J4 Actin-related protein 2/3 complex subunit 4 Schizosaccharomyces pombe 0.019637695 1 LEVO MSNTLRPYLNAVRSTLTASLALEEFSSEIVERQSQPEVEVGRSPEILLKPLVVSRNEQEQCLIESSVNSVRFSIRIKQVD EIERILVRKFMQFLMGRAESFFILRRKPVQGYDISFLITNYHTEEMLKHKLVDFIIEFMEEVDAEISEMKLFLNGRARLV AETYLSCF Q92352 Actin-related protein 2/3 complex subunit 5 Schizosaccharomyces pombe 0.016922059 1 LEVO MTFRTLDVDSITEPVLTEQDIFPIRNETAEQVQAAVSQLIPQARSAIQTGNALQGLKTLLSYVPYGNDVQEVRTQYLNAF VDVLSNIRAADIPAFVKECSTEEIDNIVNFIYRGLANPQAYNSSVLLNWHEKVVEISGIGCIVRVLNSRPDL Q10316 Actin, alpha skeletal muscle Oryctolagus cuniculus 0.042109972999999995 8 LEVO MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIE(HIC)G IITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLD SGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSS SLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQ KEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF P68135 3.6.4.- ADENOSINE-5'-DIPHOSPHATE 0.000427201 9 ADP MAGNESIUM ION 2.4305e-05 10 MG BERYLLIUM TRIFLUORIDE ION 6.600700000000001e-05 7 BEF ADENOSINE-5'-TRIPHOSPHATE 0.000507181 1 ATP water 1.8015e-05 5 HOH singleParticle particle 7.5 Quantifoil R1.2/1.3 GOLD 300 GOLD HOLEY

Grids were not glow discharged

ETHANE 100 277 FEI VITROBOT MARK IV

The samples were incubated on the grid for 50 s and the extra solution was blotted using two Vitrobot filter papers (0.55/20 mm, Grade 595, Ted Pella) for 4 s at 0 blot force. The grids were plunged into liquid ethane at ~180 degrees C with a wait time of 0.5 s..

Actin monomers with bound Ca2+ were converted to Mg2+-actin by equilibrating with 50 micromolar MgCl2 and 0.2 mM EGTA (pH 7.5) for 10 min on ice. Actin was polymerized in the presence of capping protein (CP) by sequentially mixing 8.75 micromolar Mg-ATP-actin monomers with 0.75 micromolar CP and equilibrated at room temperature for 1 h. In parallel, Arp2/3 complex (0.4 micromolar) in QB buffer was activated by mixing 0.85 micromolar GCN4-VCA and 50 micromolar ATP and incubated at 4 degrees for 1 h. The capped actin filaments sample was then gently mixed with an equal volume of activated Arp2/3 complex sample using cut pipette tips and equilibrated at 4 degrees for 5 min. Daughter filaments were formed and elongated in the presence of CP by adding 0.25 micromolar Mg-actin monomers, 50 micromolar ATP, and 40 nM CP and incubated for 5 min at room temperature. This step was subsequently repeated 4 more times, then aged for ~90 min before preparing grids for cryo-EM data collection. A final concentration of 2 mM BeFx (prepared using 2 mM BeSO4 and 10 mM NaF) was added during the 4th step of daughter filament formation (as mentioned above).

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.2 2.5 64000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Quantum LS 20

Electron micrographs for image reconstructions were collected using Titan Krios equipped with X-cold field emission gun at 300 kV, Gatan image filter with slit width of 20 eV and a nanoprobe.

The vitrified grids were screened for sample homogeneity and ice thickness in a Glacios 200 kV transmission electron microscope equipped with Gatan K2 summit camera. Electron micrographs for image reconstructions were collected using Titan Krios equipped with X-cold field emission gun at 300 kV, Gatan image filter with slit width of 20 eV and a nanoprobe.

GATAN K3 (6k x 4k) 8519 3.3 51.4

Each movie contains 41 frames with a frame time of 0.08 s. A dose rate of 28.4 counts/pixel/s and a physical pixel size of 1.346 Angstroms was used.

1 3000000 PHASE FLIPPING AND AMPLITUDE CORRECTION

These particles were subjected to 3-dimensional structure refinement and classification using 'Ab-initio 3D reconstruction' (10 classes)

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