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- EMDB-46913: local refinement of Arp3 and ArpC2 -

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Basic information

Entry
Database: EMDB / ID: EMD-46913
Titlelocal refinement of Arp3 and ArpC2
Map datalocal refinement of Arp3 and ArpC2
Sample
  • Complex: Arp 2/3 complex bound to NPFs
    • Protein or peptide: Arp3
    • Protein or peptide: Arp2
    • Protein or peptide: ArpC1
    • Protein or peptide: ArpC2
    • Protein or peptide: ArpC3
    • Protein or peptide: ArpC4
    • Protein or peptide: ArpC5
    • Protein or peptide: Neural Wiskott-Aldrich syndrome protein 1
    • Protein or peptide: Neural Wiskott-Aldrich syndrome protein 2
Keywordsactin / arp 2-3 complex / N-WASP / nucleation promoting factor / STRUCTURAL PROTEIN
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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 5, 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_46913.png

Downloads & links

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Map

FileDownload / File: emd_46913.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement of Arp3 and ArpC2
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: 0.04
Minimum - Maximum-0.10276313 - 0.27691644
Average (Standard dev.)0.00030046236 (±0.0054339063)
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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Mask #1

Fileemd_46913_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_46913_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_46913_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: Arp3
    • Protein or peptide: Arp2
    • Protein or peptide: ArpC1
    • Protein or peptide: ArpC2
    • Protein or peptide: ArpC3
    • Protein or peptide: ArpC4
    • Protein or peptide: ArpC5
    • Protein or peptide: Neural Wiskott-Aldrich syndrome protein 1
    • Protein or peptide: Neural Wiskott-Aldrich syndrome protein 2

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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: all
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Arp3

MacromoleculeName: Arp3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK RVMKGVDDLD FFIGDEAIEK PTYATKWPIR HGIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG ERTLTGTVID SGDGVTHVIP ...String:
GRLPACVVDC GTGYTKLGYA GNTEPQFIIP SCIAIKESAK RVMKGVDDLD FFIGDEAIEK PTYATKWPIR HGIVEDWDLM ERFMEQVIFK YLRAEPEDHY FLLTEPPLNT PENREYTAEI MFESFNVPGL YIAVQAVLAL AASWTSRQVG ERTLTGTVID SGDGVTHVIP VAEGYVIGSC IKHIPIAGRD ITYFIQQLLR DREVGIPPEQ SLETAKAVKE RYSYVCPDLV KEFNKYDTDG SKWIKQYTGI NAISKKEFSI DVGYERFLGP EIFFHPEFAN PDFTQPISEV VDEVIQNCPI DVRRPLYKNI VLSGGSTMFR DFGRRLQRDL KRTVDARLKL SEELSGGRLK PKPIDVQVIT HHMQRYAVWF GGSMLASTPE FYQVCHTKKD YEEIGPSICR HNPVF

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Macromolecule #2: Arp2

MacromoleculeName: Arp2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTIKDLMV GDEASELRSM LEVNYPMENG IVRNWDDMKH LWDYTFGPEK LNIDTRNCKI LLTEPPMNPT KNREKIVEVM FETYQFSGVY VAIQAVLTLY AQGLLTGVVV DSGDGVTHIC PVYEGFSLPH ...String:
MDSQGRKVVV CDNGTGFVKC GYAGSNFPEH IFPALVGRPI IRSTIKDLMV GDEASELRSM LEVNYPMENG IVRNWDDMKH LWDYTFGPEK LNIDTRNCKI LLTEPPMNPT KNREKIVEVM FETYQFSGVY VAIQAVLTLY AQGLLTGVVV DSGDGVTHIC PVYEGFSLPH LTRRLDIAGR DITRYLIKLL LLRGYAFNHS ADFETVRMIK EKLCYVGYNI EQEQKLALET TVLVESYTLP DGRIIKVGGE RFEAPEALFQ PHLINVEGVG VAELLFNTIQ AADIDTRSEF YKHIVLSGGS TMYPGLPSRL ERELKQLYLE RVLKGDVEKL SKFKIRIEDP PRRKHMVFLG GAVLADIMKD KDNFWMTRQE YQEKGVRVLE KLG

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Macromolecule #3: ArpC1

MacromoleculeName: ArpC1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString: MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPTL VILRINRAAT FVKWSPLENK FAVGSGARLI SVCYFESEND WWVSKHIKKP IRSTVLSLDW HPNNVLLAAG SCDFKCRVFS ...String:
MSLHQFLLEP ITCHAWNRDR TQIALSPNNH EVHIYKKNGG QWVKAHELKE HNGHITGIDW APKSDRIVTC GADRNAYVWS QKDGVWKPTL VILRINRAAT FVKWSPLENK FAVGSGARLI SVCYFESEND WWVSKHIKKP IRSTVLSLDW HPNNVLLAAG SCDFKCRVFS AYIKEVDEKP ASTPWGSKMP FGQLMSEFGG SGTGGWVHGV SFSASGSRLA WVSHDSTVSV ADASKSVQVS TLKTEFLPLL SVSFVSENSV VAAGHDCCPM LFNYDDRGCL TFVSKLDIPK QSRNTALETL HQNSITQVSI YEVDKQDCRK FCTTGIDGAM TIWDFKTLES SIQGLRIM

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Macromolecule #4: ArpC2

MacromoleculeName: ArpC2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
SequenceString: MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPESG YNVSLLYDLE NLPASKDSIV HQAGMLKRNC FASVFEKYFQ FQEEGKEGEN RAVIHYRDDE TMYVESKKDR VTVVFSTVFK ...String:
MILLEVNNRI IEETLALKFE NAAAGNKPEA VEVTFADFDG VLYHISNPNG DKTKVMVSIS LKFYKELQAH GADELLKRVY GSYLVNPESG YNVSLLYDLE NLPASKDSIV HQAGMLKRNC FASVFEKYFQ FQEEGKEGEN RAVIHYRDDE TMYVESKKDR VTVVFSTVFK DDDDVVIGKV FMQEFKEGRR ASHTAPQVLF SHREPPLELK DTDAAVGDNI GYITFVLFPR HTNASARDNT INLIHTFRDY LHYHIKCSKA YIHTRMRAKT SDFLKVLNRA RPDAE

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Macromolecule #5: ArpC3

MacromoleculeName: ArpC3 / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
SequenceString:
PAYHSSLMDP DTKLIGNMAL LPIRSQFKGP APRETKDTDI VDEAIYYFKA NVFFKNYEIK NEADRTLIYI TLYISECLKK LQKCNSKSQG EKEMYTLGIT NFPIPGEPGF PLNAIYAKPA NKQEDEVMRA YLQQLRQETG LRLCEKVFDP QNDKPSKWWT CFVKRQFMNK SLSGP

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Macromolecule #6: ArpC4

MacromoleculeName: ArpC4 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
SequenceString:
TATLRPYLSA VRATLQAALC LENFSSQVVE RHNKPEVEVR SSKELLLQPV TISRNEKEKV LIEGSINSVR VSIAVKQADE IEKILCHKFM RFMMMRAENF FILRRKPVEG YDISFLITNF HTEQMYKHKL VDFVIHFMEE IDKEISEMKL SVNARARIVA EEFLKNF

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Macromolecule #7: ArpC5

MacromoleculeName: ArpC5 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
SequenceString:
NKFVDEGNMT AALQAALKNP PINTKSQAVK DRAGSIVLKV LISFKANDIE KAVQSLDKNG VDLLMKYIYK GFESPSDNSS AVLLQWHEKA LAAGGVGSIV RVLTARKTV

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Macromolecule #8: Neural Wiskott-Aldrich syndrome protein 1

MacromoleculeName: Neural Wiskott-Aldrich syndrome protein 1 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
SequenceString:
SGIVGALMEV MQKRSKAIHS SDEDEDDDEW ED

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Macromolecule #9: Neural Wiskott-Aldrich syndrome protein 2

MacromoleculeName: Neural Wiskott-Aldrich syndrome protein 2 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
SequenceString:
SGIVGALMEV MQKRSKAIHS SDEEDFEDDD EWED

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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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292625
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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