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- EMDB-27962: Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction -

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Basic information

Entry
Database: EMDB / ID: EMD-27962
TitleCryo-EM structure of S. pombe Arp2/3 complex in the branch junction
Map datarelion map
Sample
  • Complex: S. pombe Arp2/3 complex in actin branch junction
    • Complex: S. pombe Arp2/3 complex in actin branch junction
      • Protein or peptide: x 7 types
    • Complex: chicken skeletal muscle actin in branch junction
      • Protein or peptide: x 1 types
  • Ligand: x 3 types
Function / homology
Function and homology information


Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / actin cortical patch organization / Clathrin-mediated endocytosis / Neutrophil degranulation / medial cortex / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation ...Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / actin cortical patch organization / Clathrin-mediated endocytosis / Neutrophil degranulation / medial cortex / cell cortex of cell tip / actin cortical patch assembly / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin cortical patch / cell tip / Striated Muscle Contraction / regulation of actin filament polymerization / mating projection tip / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / cell division site / skeletal muscle thin filament assembly / striated muscle thin filament / mitotic cytokinesis / skeletal muscle fiber development / stress fiber / actin filament polymerization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / endocytosis / actin filament binding / hydrolase activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Actin-related protein 2/3 complex subunit 5 / 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 ...Actin-related protein 2/3 complex subunit 5 / 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 16 kDa subunit (p16-Arc) / ARP2/3 complex 20 kDa subunit (ARPC4) / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin-related protein 2/3 complex subunit 2 / Actin-related protein 3 / Actin, alpha skeletal muscle / Actin-related protein 2/3 complex subunit 1 / Actin-related protein 2/3 complex subunit 5 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2 / Actin-related protein 2/3 complex subunit 3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / Gallus gallus (chicken) / fission yeast (fission yeast) / Fission yeast (fission yeast) / chicken (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChou SZ / Pollard TP
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM026132 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM026338 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Mechanism of actin filament branch formation by Arp2/3 complex revealed by a high-resolution cryo-EM structureof the branch junction.
Authors: Steven Z Chou / Moon Chatterjee / Thomas D Pollard /
Abstract: We reconstructed the structure of actin filament branch junctions formed by fission yeast Arp2/3 complex at 3.5 Å resolution from images collected by electron cryo-microscopy. During specimen ...We reconstructed the structure of actin filament branch junctions formed by fission yeast Arp2/3 complex at 3.5 Å resolution from images collected by electron cryo-microscopy. During specimen preparation, all of the actin subunits and Arp3 hydrolyzed their bound adenosine triphosphate (ATP) and dissociated the γ-phosphate, but Arp2 retained the γ-phosphate. Binding tightly to the side of the mother filament and nucleating the daughter filament growing as a branch requires Arp2/3 complex to undergo a dramatic conformational change where two blocks of structure rotate relative to each other about 25° to align Arp2 and Arp3 as the first two subunits in the branch. During branch formation, Arp2/3 complex acquires more than 8,000 Å of new buried surface, accounting for the stability of the branch. Inactive Arp2/3 complex binds only transiently to the side of an actin filament, because its conformation allows only a subset of the interactions found in the branch junction.
History
DepositionAug 26, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27962.png

Downloads & links

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Map

FileDownload / File: emd_27962.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrelion map
Voxel sizeX=Y=Z: 1.364 Å
Density
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.07896913 - 0.16487019
Average (Standard dev.)0.0003627558 (±0.004060604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 409.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27962_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer map

Fileemd_27962_additional_1.map
AnnotationDeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_27962_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_27962_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. pombe Arp2/3 complex in actin branch junction

EntireName: S. pombe Arp2/3 complex in actin branch junction
Components
  • Complex: S. pombe Arp2/3 complex in actin branch junction
    • Complex: S. pombe Arp2/3 complex in actin branch junction
      • Protein or peptide: Actin-related protein 3
      • Protein or peptide: Actin-related protein 2
      • Protein or peptide: Actin-related protein 2/3 complex subunit 1
      • 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
    • Complex: chicken skeletal muscle actin in branch junction
      • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: S. pombe Arp2/3 complex in actin branch junction

SupramoleculeName: S. pombe Arp2/3 complex in actin branch junction / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#8

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Supramolecule #2: S. pombe Arp2/3 complex in actin branch junction

SupramoleculeName: S. pombe Arp2/3 complex in actin branch junction / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#7
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Supramolecule #3: chicken skeletal muscle actin in branch junction

SupramoleculeName: chicken skeletal muscle actin in branch junction / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #8
Source (natural)Organism: Gallus gallus (chicken)

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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: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 47.427137 KDa
SequenceString: MASFNVPIIM DNGTGYSKLG YAGNDAPSYV FPTVIATRSA GASSGPAVSS KPSYMASKGS GHLSSKRATE DLDFFIGNDA LKKASAGYS LDYPIRHGQI ENWDHMERFW QQSLFKYLRC EPEDHYFLLT EPPLNPPENR ENTAEIMFES FNCAGLYIAV Q AVLALAAS ...String:
MASFNVPIIM DNGTGYSKLG YAGNDAPSYV FPTVIATRSA GASSGPAVSS KPSYMASKGS GHLSSKRATE DLDFFIGNDA LKKASAGYS LDYPIRHGQI ENWDHMERFW QQSLFKYLRC EPEDHYFLLT EPPLNPPENR ENTAEIMFES FNCAGLYIAV Q AVLALAAS WTSSKVTDRS LTGTVVDSGD GVTHIIPVAE GYVIGSSIKT MPLAGRDVTY FVQSLLRDRN EPDSSLKTAE RI KEECCYV CPDIVKEFSR FDREPDRYLK YASESITGHS TTIDVGFERF LAPEIFFNPE IASSDFLTPL PELVDNVVQS SPI DVRKGL YKNIVLSGGS TLFKNFGNRL QRDLKRIVDE RIHRSEMLSG AKSGGVDVNV ISHKRQRNAV WFGGSLLAQT PEFG SYCHT KADYEEYGAS IARRYQIFGN SL

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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: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 44.286758 KDa
SequenceString: MESAPIVLDN GTGFVKVGYA KDNFPRFQFP SIVGRPILRA EEKTGNVQIK DVMVGDEAEA VRSLLQVKYP MENGIIRDFE EMNQLWDYT FFEKLKIDPR GRKILLTEPP MNPVANREKM CETMFERYGF GGVYVAIQAV LSLYAQGLSS GVVVDSGDGV T HIVPVYES ...String:
MESAPIVLDN GTGFVKVGYA KDNFPRFQFP SIVGRPILRA EEKTGNVQIK DVMVGDEAEA VRSLLQVKYP MENGIIRDFE EMNQLWDYT FFEKLKIDPR GRKILLTEPP MNPVANREKM CETMFERYGF GGVYVAIQAV LSLYAQGLSS GVVVDSGDGV T HIVPVYES VVLNHLVGRL DVAGRDATRY LISLLLRKGY AFNRTADFET VREMKEKLCY VSYDLELDHK LSEETTVLMR NY TLPDGRV IKVGSERYEC PECLFQPHLV GSEQPGLSEF IFDTIQAADV DIRKYLYRAI VLSGGSSMYA GLPSRLEKEI KQL WFERVL HGDPARLPNF KVKIEDAPRR RHAVFIGGAV LADIMAQNDH MWVSKAEWEE YGVRALDKLG PRTT

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

MacromoleculeName: Actin-related protein 2/3 complex subunit 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 41.643465 KDa
SequenceString: MATSQVLHIL PKPSYEHAFN SQRTEFVTTT ATNQVELYEQ DGNGWKHART FSDHDKIVTC VDWAPKSNRI VTCSQDRNAY VYEKRPDGT WKQTLVLLRL NRAATFVRWS PNEDKFAVGS GARVISVCYF EQENDWWVSK HLKRPLRSTI LSLDWHPNNV L LAAGCADR ...String:
MATSQVLHIL PKPSYEHAFN SQRTEFVTTT ATNQVELYEQ DGNGWKHART FSDHDKIVTC VDWAPKSNRI VTCSQDRNAY VYEKRPDGT WKQTLVLLRL NRAATFVRWS PNEDKFAVGS GARVISVCYF EQENDWWVSK HLKRPLRSTI LSLDWHPNNV L LAAGCADR KAYVLSAYVR DVDAKPEASV WGSRLPFNTV CAEYPSGGWV HAVGFSPSGN ALAYAGHDSS VTIAYPSAPE QP PRALITV KLSQLPLRSL LWANESAIVA AGYNYSPILL QGNESGWAHT RDLDAGTSKT SFTHTGNTGE GREEEGPVSF TAL RSTFRN MDLKGSSQSI SSLPTVHQNM IATLRPYAGT PGNITAFTSS GTDGRVVLWT L

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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: Fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 37.02523 KDa
SequenceString: MLSLDYNNIF IYELLTERFS SENPSSIDQV VTDFDGVTFH ISTPEEKTKI LISLSMKCYP ELVNYGTLDL LKQIYGAYVH EPEMGYNFS ILIDLQQLPA TDEEKEQLAM SISMLKRNVL AAPFHRAFTK QAELADLARK DPENAPMLDK QATSQELMAI H YRDEETIV ...String:
MLSLDYNNIF IYELLTERFS SENPSSIDQV VTDFDGVTFH ISTPEEKTKI LISLSMKCYP ELVNYGTLDL LKQIYGAYVH EPEMGYNFS ILIDLQQLPA TDEEKEQLAM SISMLKRNVL AAPFHRAFTK QAELADLARK DPENAPMLDK QATSQELMAI H YRDEETIV LWPEHDRVTV VFSTKFREET DRIFGKVFLQ EFVDARRRPA IQTAPQVLFS YRDPPLEIRD IQGIQKGDDF GF VTFVLFE RHFTPQNRED CISHIQVFRN TLHFHIKASK AYMHQRMRKR VADFQKVLNR AKPDVELERK TATGRSFVRA

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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: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 19.865746 KDa
SequenceString:
MPAYHSSFLS LTDVPTTGNI AMLPLKTKFR GPAYPADESQ MDIIDECIGL FRANCFFRNF EIKGPADRTL IYGTLFISEC LGRVNGLNY RDAERQLNSL ALENFSIPGS AGFPLNALYA PPLSPQDAEI MRTYLTQFRQ ELAYRLLSHV YATEKDHPSK W WTCFSKRR FMNKAL

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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: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 19.637695 KDa
SequenceString:
MSNTLRPYLN AVRSTLTASL ALEEFSSEIV ERQSQPEVEV GRSPEILLKP LVVSRNEQEQ CLIESSVNSV RFSIRIKQVD EIERILVRK FMQFLMGRAE SFFILRRKPV QGYDISFLIT NYHTEEMLKH KLVDFIIEFM EEVDAEISEM KLFLNGRARL V AETYLSCF

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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: fission yeast (fission yeast) / Strain: 972 / ATCC 24843
Molecular weightTheoretical: 16.922059 KDa
SequenceString:
MTFRTLDVDS ITEPVLTEQD IFPIRNETAE QVQAAVSQLI PQARSAIQTG NALQGLKTLL SYVPYGNDVQ EVRTQYLNAF VDVLSNIRA ADIPAFVKEC STEEIDNIVN FIYRGLANPQ AYNSSVLLNW HEKVVEISGI GCIVRVLNSR PDL

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Macromolecule #8: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 8 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: chicken (chicken)
Molecular weightTheoretical: 41.875633 KDa
SequenceString: DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DEDETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VMSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ITKQEYDEAG PSIVHRKCF

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 9 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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
Component:
ConcentrationFormulaName
100.0 mMKClpotassium chloride
1.0 mMMgCl2Magnesium chloride
1.0 mMC14H24N2O10EGTA
10.0 mMC8H18N2O4SHEPES
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 4200 / Average exposure time: 3.28 sec. / Average electron dose: 50.07 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.9 µm / Calibrated defocus min: 0.9 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 36657
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 131393
Startup modelType of model: EMDB MAP
EMDB ID:

11869

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 79467
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

1k8k

,

6djo

,

6w17

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-8e9b:
Cryo-EM structure of S. pombe Arp2/3 complex in the branch junction

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