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- EMDB-46992: Bovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1 -

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Basic information

Entry
Database: EMDB / ID: EMD-46992
TitleBovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1
Map dataBovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1
Sample
  • Complex: Arp 2/3 complex bound to NPFs
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1A
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5
    • Protein or peptide: Actin nucleation-promoting factor WASL
  • Protein or peptide: Actin-related protein 3
  • Protein or peptide: Actin-related protein 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / arp 2-3 complex / N-WASP / nucleation promoting factor / STRUCTURAL PROTEIN
Function / homology
Function and homology information


negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / negative regulation of lymphocyte migration / Arp2/3 complex-mediated actin nucleation ...negative regulation of membrane tubulation / spindle localization / positive regulation of clathrin-dependent endocytosis / muscle cell projection membrane / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / Arp2/3 protein complex / negative regulation of lymphocyte migration / Arp2/3 complex-mediated actin nucleation / vesicle transport along actin filament / GTPase regulator activity / NOSTRIN mediated eNOS trafficking / actin cap / vesicle organization / regulation of actin filament polymerization / Clathrin-mediated endocytosis / vesicle budding from membrane / dendritic spine morphogenesis / actin polymerization or depolymerization / protein-containing complex localization / Nephrin family interactions / DCC mediated attractive signaling / regulation of postsynapse organization / Neutrophil degranulation / positive regulation of filopodium assembly / RHOV GTPase cycle / RHOJ GTPase cycle / positive regulation of actin filament polymerization / RHOQ GTPase cycle / CDC42 GTPase cycle / cilium assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / actin filament polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / cell projection / response to bacterium / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / actin filament binding / endocytic vesicle membrane / synaptic vesicle membrane / cell migration / lamellipodium / actin cytoskeleton / Clathrin-mediated endocytosis / regulation of protein localization / site of double-strand break / actin binding / actin cytoskeleton organization / protein-containing complex assembly / cytoplasmic vesicle / cell cortex / postsynapse / neuron projection / endosome / cell division / focal adhesion / endoplasmic reticulum membrane / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily ...Actin nucleation-promoting factor WAS, C-terminal / WASP family, EVH1 domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain profile. / WH2 domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / PH-like domain superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin-related protein 2 / Actin nucleation-promoting factor WASL / Actin-related protein 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1A / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 3
Similarity search - Component
Biological speciesBos taurus (domestic cattle) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsSaks AJ / Barrie KR / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM073791-19 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail and conformational changes in Arp2/3 complex.
Authors: Andrew J Saks / Kyle R Barrie / Grzegorz Rebowski / Roberto Dominguez /
Abstract: Arp2/3 complex generates branched actin networks essential for numerous motile functions of the cell. It comprises seven subunits: actin-related proteins (Arps) 2 and 3 and five scaffolding subunits ...Arp2/3 complex generates branched actin networks essential for numerous motile functions of the cell. It comprises seven subunits: actin-related proteins (Arps) 2 and 3 and five scaffolding subunits (ArpC1-5). The complex adopts two major conformations: inactive, with the Arps interacting end-to-end, and active, with the Arps aligned side-by-side like subunits in the actin filament. Activation involves several cofactors, including ATP, WASP-family nucleation-promoting factors (NPFs), actin monomers, and the mother actin filament. NPFs bind to two sites, one on Arp2-ArpC1 and one on Arp3, delivering actin subunits at the barbed end of the Arps to initiate branch elongation. However, the mechanisms by which each NPF drives the equilibrium toward activation remain unclear. We present two cryo-electron microscopy (cryo-EM) structures of Arp2/3 complex at 2.9-Å resolution: one with NPFs bound to Arp3 and ArpC1 but not Arp2 and another with NPFs bound to Arp3 and Arp2-ArpC1. The structures reveal that NPF binding to Arp2 is allosterically linked to the release of ArpC5's N-terminal tail from Arp2 and conformational changes in Arp2, including closure of its ATP-binding cleft and partial rotation and translation toward its position in the active complex at the branch. Previous work identified another allosteric switch linking NPF binding to Arp3 with the release of its inhibitory C-terminal tail, which we also observe. In summary, both NPF-binding sites induce allosteric changes in Arp2/3 complex, collectively shifting the equilibrium toward activation.
History
DepositionSep 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46992.png

Downloads & links

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Map

FileDownload / File: emd_46992.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å		0.86 Å/pix.
x 352 pix.
= 302.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum0.0 - 0.23731111
Average (Standard dev.)0.00090482994 (±0.0062224697)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 302.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Arp 2/3 complex bound to NPFs

EntireName: Arp 2/3 complex bound to NPFs
Components
  • Complex: Arp 2/3 complex bound to NPFs
    • Protein or peptide: Actin-related protein 2/3 complex subunit 1A
    • Protein or peptide: Actin-related protein 2/3 complex subunit 2
    • Protein or peptide: Actin-related protein 2/3 complex subunit 3
    • Protein or peptide: Actin-related protein 2/3 complex subunit 4
    • Protein or peptide: Actin-related protein 2/3 complex subunit 5
    • Protein or peptide: Actin nucleation-promoting factor WASL
  • Protein or peptide: Actin-related protein 3
  • Protein or peptide: Actin-related protein 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Arp 2/3 complex bound to NPFs

SupramoleculeName: Arp 2/3 complex bound to NPFs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#8
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Actin-related protein 3

MacromoleculeName: Actin-related protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 46.851305 KDa
SequenceString: GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK VGDQAQRRVM KGVDDLDFFI GDEAIEKPTY ATKWPIRHGI VEDWDLMER FMEQVIFKYL RAEPEDHYFL LTEPPLNTPE NREYTAEIMF ESFNVPGLYI AVQAVLALAA SWTSRQVGER T LTGTVIDS ...String:
GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK VGDQAQRRVM KGVDDLDFFI GDEAIEKPTY ATKWPIRHGI VEDWDLMER FMEQVIFKYL RAEPEDHYFL LTEPPLNTPE NREYTAEIMF ESFNVPGLYI AVQAVLALAA SWTSRQVGER T LTGTVIDS GDGVTHVIPV AEGYVIGSCI KHIPIAGRDI TYFIQQLLRD REVGIPPEQS LETAKAVKER YSYVCPDLVK EF NKYDTDG SKWIKQYTGI NAISKKEFSI DVGYERFLGP EIFFHPEFAN PDFTQPISEV VDEVIQNCPI DVRRPLYKNI VLS GGSTMF RDFGRRLQRD LKRTVDARLK LSEELSGGRL KPKPIDVQVI THHMQRYAVW FGGSMLASTP EFYQVCHTKK DYEE IGPSI CRHNPVF

UniProtKB: Actin-related protein 3

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Macromolecule #2: Actin-related protein 2

MacromoleculeName: Actin-related protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 44.362152 KDa
SequenceString: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP ...String:
MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTTKVGNI EIKDLMVGDE ASELRSMLEV NYPMENGIVR NWDDMKHLW DYTFGPEKLN IDTRNCKILL TEPPMNPTKN REKIVEVMFE TYQFSGVYVA IQAVLTLYAQ GLLTGVVVDS G DGVTHICP VYEGFSLPHL TRRLDIAGRD ITRYLIKLLL LRGYAFNHSA DFETVRMIKE KLCYVGYNIE QEQKLALETT VL VESYTLP DGRIIKVGGE RFEAPEALFQ PHLINVEGVG VAELLFNTIQ AADIDTRSEF YKHIVLSGGS TMYPGLPSRL ERE LKQLYL ERVLKGDVEK LSKFKIRIED PPRRKHMVFL GGAVLADIMK DKDNFWMTRQ EYQEKGVRVL EKLG

UniProtKB: Actin-related protein 2

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Macromolecule #3: Actin-related protein 2/3 complex subunit 1A

MacromoleculeName: Actin-related protein 2/3 complex subunit 1A / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 41.594238 KDa
SequenceString: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL ISVCYFESEN DWWVSKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRV ...String:
MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPT LVILRINRAA TFVKWSPLEN KFAVGSGARL ISVCYFESEN DWWVSKHIKK PIRSTVLSLD WHPNNVLLAA G SCDFKCRV FSAYIKEVDE KPASTPWGSK MPFGQLMSEF GGSGTGGWVH GVSFSASGSR LAWVSHDSTV SVADASKSVQ VS TLKTEFL PLLSVSFVSE NSVVAAGHDC CPMLFNYDDR GCLTFVSKLD IPKQSIQRNM SAMERFRNMD KRATTEDRNT ALE TLHQNS ITQVSIYEVD KQDCRKFCTT GIDGAMTIWD FKTLESSIQG LRIM

UniProtKB: Actin-related protein 2/3 complex subunit 1A

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Macromolecule #4: Actin-related protein 2/3 complex subunit 2

MacromoleculeName: Actin-related protein 2/3 complex subunit 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 32.672973 KDa
SequenceString: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV ...String:
MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPES GYNVSLLYDL ENLPASKDSI VHQAGMLKRN CFASVFEKYF QFQEEGKEGE NRAVIHYRDD ETMYVESKKD R VTVVFSTV FKDDDDVVIG KVFMQEFKEG RRASHTAPQV LFSHREPPLE LKDTDAAVGD NIGYITFVLF PRHTNASARD NT INLIHTF RDYLHYHIKC SKAYIHTRMR AKTSDFLKVL NRARPDAE

UniProtKB: Actin-related protein 2/3 complex subunit 2

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Macromolecule #5: Actin-related protein 2/3 complex subunit 3

MacromoleculeName: Actin-related protein 2/3 complex subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 20.256287 KDa
SequenceString:
PAYHSSLMDP DTKLIGNMAL LPIRSQFKGP APRETKDTDI VDEAIYYFKA NVFFKNYEIK NEADRTLIYI TLYISECLKK LQKCNSKSQ GEKEMYTLGI TNFPIPGEPG FPLNAIYAKP ANKQEDEVMR AYLQQLRQET GLRLCEKVFD PQNDKPSKWW T CFVKRQFM NKSLSGP

UniProtKB: Actin-related protein 2/3 complex subunit 3

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Macromolecule #6: Actin-related protein 2/3 complex subunit 4

MacromoleculeName: Actin-related protein 2/3 complex subunit 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 19.565852 KDa
SequenceString:
TATLRPYLSA VRATLQAALC LENFSSQVVE RHNKPEVEVR SSKELLLQPV TISRNEKEKV LIEGSINSVR VSIAVKQADE IEKILCHKF MRFMMMRAEN FFILRRKPVE GYDISFLITN FHTEQMYKHK LVDFVIHFME EIDKEISEMK LSVNARARIV A EEFLKNF

UniProtKB: Actin-related protein 2/3 complex subunit 4

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Macromolecule #7: Actin-related protein 2/3 complex subunit 5

MacromoleculeName: Actin-related protein 2/3 complex subunit 5 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 16.251308 KDa
SequenceString:
MSKNTVSSAR FRKVDVGEYD ENKFVDEEDG GDGQAGPDEG EVDSCLRQGN MTAALQAALK NPPINTKSQA VKDRAGSIVL KVLISFKAN DIEKAVQSLD KNGVDLLMKY IYKGFESPSD NSSAVLLQWH EKALAAGGVG SIVRVLTARK TV

UniProtKB: Actin-related protein 2/3 complex subunit 5

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Macromolecule #8: Actin nucleation-promoting factor WASL

MacromoleculeName: Actin nucleation-promoting factor WASL / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.750827 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGIVGALMEV MQKRSKAIHS SDEDEDEDDE EDFEDDDEWE D

UniProtKB: Actin nucleation-promoting factor WASL

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: OTHER / Average electron dose: 47.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292065
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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