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- PDB-7aqk: Model of the actin filament Arp2/3 complex branch junction in cells -

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Basic information

Entry
Database: PDB / ID: 7aqk
TitleModel of the actin filament Arp2/3 complex branch junction in cells
Components
  • (Actin-related protein ...) x 7
  • Actin, alpha skeletal muscle, ACTA1
KeywordsSTRUCTURAL PROTEIN / Actin / Arp2-3 complex / Cytoskeleton
Function / homology
Function and homology information


podosome core / concave side of sperm head / apical ectoplasmic specialization / basal ectoplasmic specialization / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex ...podosome core / concave side of sperm head / apical ectoplasmic specialization / basal ectoplasmic specialization / actin filament branch point / ventral surface of cell / microtubule organizing center localization / negative regulation of bleb assembly / positive regulation of barbed-end actin filament capping / apical tubulobulbar complex / tubulobulbar complex / regulation of myosin II filament organization / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / peripheral region of growth cone / meiotic cytokinesis / protein kinase C signaling / lamellipodium organization / muscle cell projection membrane / spindle localization / skeletal muscle fiber adaptation / postsynaptic actin cytoskeleton organization / leading edge of lamellipodium / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / hemidesmosome / Striated Muscle Contraction / actin filament network formation / Arp2/3 protein complex / asymmetric cell division / postsynapse organization / Arp2/3 complex-mediated actin nucleation / cellular response to rapamycin / podosome ring / actin cap / negative regulation of axon extension / Regulation of actin dynamics for phagocytic cup formation / maintenance of cell polarity / Clathrin-mediated endocytosis / regulation of actin filament polymerization / positive regulation of dendritic spine morphogenesis / positive regulation of astrocyte differentiation / cellular response to potassium ion / positive regulation of dendrite morphogenesis / apical dendrite / astrocyte differentiation / positive regulation of synapse assembly / positive regulation of podosome assembly / positive regulation of fibroblast migration / response to steroid hormone / positive regulation of filopodium assembly / podosome / smooth muscle cell migration / positive regulation of actin filament polymerization / positive regulation of smooth muscle cell migration / establishment or maintenance of cell polarity / mesenchyme migration / cell leading edge / regulation of synaptic vesicle endocytosis / filamentous actin / brush border / striated muscle thin filament / skeletal muscle thin filament assembly / excitatory synapse / cilium assembly / positive regulation of protein targeting to membrane / glutamate receptor binding / positive regulation of double-strand break repair via homologous recombination / response to mechanical stimulus / stress fiber / skeletal muscle fiber development / positive regulation of lamellipodium assembly / cellular response to transforming growth factor beta stimulus / cytoskeletal protein binding / ruffle / cellular response to platelet-derived growth factor stimulus / axon terminus / positive regulation of substrate adhesion-dependent cell spreading / Neutrophil degranulation / actin filament polymerization / cellular response to epidermal growth factor stimulus / positive regulation of neuron differentiation / secretory granule / dendritic shaft / filopodium / cell projection / meiotic cell cycle / actin filament / positive regulation of protein localization to plasma membrane / regulation of actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / structural constituent of cytoskeleton / cellular response to type II interferon / ruffle membrane / synaptic vesicle membrane / actin filament binding / cell migration / cell-cell junction
Similarity search - Function
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 ...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) / 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 4 / Actin-related protein 2 / Actin, alpha skeletal muscle / Actin-related protein 3 / 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 1B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9 Å
AuthorsFaessler, F. / Dimchev, G. / Hodirnau, V.V. / Wan, W. / Schur, F.K.M.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33367 Austria
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction.
Authors: Florian Fäßler / Georgi Dimchev / Victor-Valentin Hodirnau / William Wan / Florian K M Schur /
Abstract: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves ...The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
b: Actin-related protein 2, Arp2
a: Actin-related protein 3, Arp3
c: Actin-related protein 2/3 complex subunit 1b, ArpC1b
d: Actin-related protein 2/3 complex subunit 2, ArpC2
e: Actin-related protein 2/3 complex subunit 3, ArpC3
f: Actin-related protein 2/3 complex subunit 4, ArpC4
g: Actin-related protein 2/3 complex subunit 5, ArpC5
h: Actin, alpha skeletal muscle, ACTA1
i: Actin, alpha skeletal muscle, ACTA1
j: Actin, alpha skeletal muscle, ACTA1
k: Actin, alpha skeletal muscle, ACTA1
l: Actin, alpha skeletal muscle, ACTA1
m: Actin, alpha skeletal muscle, ACTA1
n: Actin, alpha skeletal muscle, ACTA1
o: Actin, alpha skeletal muscle, ACTA1
p: Actin, alpha skeletal muscle, ACTA1
q: Actin, alpha skeletal muscle, ACTA1
r: Actin, alpha skeletal muscle, ACTA1


Theoretical massNumber of molelcules
Total (without water)687,29718
Polymers687,29718
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Actin-related protein ... , 7 types, 7 molecules bacdefg

#1: Protein Actin-related protein 2, Arp2


Mass: 44818.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P61161*PLUS
#2: Protein Actin-related protein 3, Arp3


Mass: 47428.031 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus I259V / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q99JY9*PLUS
#3: Protein Actin-related protein 2/3 complex subunit 1b, ArpC1b


Mass: 41016.738 Da / Num. of mol.: 1
Mutation: From Bos taurus to Mus Musculus V43N, Q44K, V58I, D63E, K109N, S154N, N213S, A229V, S256N, S274N, G277V, K278T, L296M, S313G, A216T, R360K
Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9WV32*PLUS
#4: Protein Actin-related protein 2/3 complex subunit 2, ArpC2


Mass: 34402.043 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus Y84F, S90P / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9CVB6*PLUS
#5: Protein Actin-related protein 2/3 complex subunit 3, ArpC3


Mass: 20572.666 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus I24L / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9JM76*PLUS
#6: Protein Actin-related protein 2/3 complex subunit 4, ArpC4


Mass: 19697.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P59999*PLUS
#7: Protein Actin-related protein 2/3 complex subunit 5, ArpC5


Mass: 16295.317 Da / Num. of mol.: 1 / Mutation: From Bos taurus to Mus Musculus D28E / Source method: isolated from a natural source
Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they ...Details: As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: Q9CPW4*PLUS

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Protein , 1 types, 11 molecules hijklmnopqr

#8: Protein
Actin, alpha skeletal muscle, ACTA1


Mass: 42096.953 Da / Num. of mol.: 11 / Source method: isolated from a natural source
Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even ...Details: As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
Source: (natural) Mus musculus (house mouse) / Cell line: NIH-3T3 / References: UniProt: P68134*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Actin Filament Arp2/3 Complex Branch Junction / Type: CELL
Details: Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia
Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse) / Cellular location: Lamellipodium
Buffer solutionpH: 6.1 / Details: Adjust to pH 6.1 using NaOH
Buffer component
IDConc.NameBuffer-ID
110 mMMES1
2150 mMsodium chloride1
35 mMEGTA1
45 mMGlucose1
55 mMMagnesium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin
Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 277 K
Details: Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: -5.5 nm / Nominal defocus min: -1.75 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.21 sec. / Electron dose: 2.79 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
Details: Images were collected in movie-mode at 7 frames per tilt
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Dynamo1.133volume selection
2Warp1.07volume selection
3SerialEMimage acquisition
5Warp1.07CTF correction
8UCSF Chimera1.13.1model fitting
11RELION3.0.9final Euler assignment
12RELION3.0.9classification
13RELION3.0.93D reconstruction
14ISOLDE1.0b5model refinement
15Coot0.8.9.3model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14296
Details: Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: Template Matching
Details: After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained.
Num. of tomograms: 131 / Num. of volumes extracted: 39300
Reference model: Reference generated from manually selected particles
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
11TYQ

1tyq

A1TYQ12-39
21TYQ

1tyq

A1TYQ152-353
31TYQ

1tyq

A1TYQ1360-418
41TYQ

1tyq

B1TYQ1151-345
51TYQ

1tyq

C1TYQ11-288
61TYQ

1tyq

C1TYQ1319-372
71TYQ

1tyq

D1TYQ11-208
81TYQ

1tyq

D1TYQ1217-281
91TYQ

1tyq

E1TYQ12-150
101TYQ

1tyq

E1TYQ1155-174
111TYQ

1tyq

F1TYQ13-168
121TYQ

1tyq

G1TYQ136-151
134JD2

4jd2

B4JD224-150
144JD2

4jd2

B4JD22346-387
151K8K

1k8k

C1K8K3297-309
166T20

6t20

A6T2045-375
176T20

6t20

B6T2045-375
186T20

6t20

C6T2045-375
196T20

6t20

D6T2045-375
206T20

6t20

E6T2045-375

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