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- EMDB-5354: Remodeling of actin filaments by ADF-cofilin proteins -

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Basic information

Entry
Database: EMDB / ID: EMD-5354
TitleRemodeling of actin filaments by ADF-cofilin proteins
Map dataThis is the reconstructed volume of the actin-cofilin complex.
Sample
  • Sample: actin decorated with cofilin
  • Protein or peptide: F-Actin
  • Protein or peptide: cofilin-2
Keywordsactin / cofilin / helical polymers
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / RHO GTPases activate IQGAPs / Adherens junctions interactions / DNA Damage Recognition in GG-NER / Clathrin-mediated endocytosis / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape ...Gap junction degradation / Formation of annular gap junctions / RHO GTPases activate IQGAPs / Adherens junctions interactions / DNA Damage Recognition in GG-NER / Clathrin-mediated endocytosis / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / RHO GTPases Activate Formins / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / UCH proteinases / B-WICH complex positively regulates rRNA expression / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / RHOF GTPase cycle / actin filament fragmentation / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of actin filament depolymerization / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of synaptic plasticity / EPH-ephrin mediated repulsion of cells / negative regulation of actin filament depolymerization / MAP2K and MAPK activation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / actin filament severing / structural constituent of postsynaptic actin cytoskeleton / dense body / establishment of spindle localization / regulation of dendritic spine morphogenesis / host-mediated activation of viral process / cell projection organization / actin filament depolymerization / negative regulation of cell motility / negative regulation of cell adhesion / RHO GTPases Activate ROCKs / negative regulation of cell size / cellular response to interleukin-6 / regulation of cell morphogenesis / negative regulation of dendritic spine maintenance / neural crest cell migration / positive regulation of cell motility / cortical actin cytoskeleton / cellular response to insulin-like growth factor stimulus / phosphatidylinositol bisphosphate binding / establishment of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of dendritic spine development / mitotic cytokinesis / lamellipodium membrane / positive regulation of proteolysis / Sema3A PAK dependent Axon repulsion / cellular response to interleukin-1 / positive regulation of focal adhesion assembly / response to amino acid / postsynaptic density, intracellular component / Rho protein signal transduction / positive regulation of lamellipodium assembly / cytoskeleton organization / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / synaptic membrane / cellular response to epidermal growth factor stimulus / response to activity / actin filament / hippocampus development / filopodium / cell motility / mitochondrial membrane / Regulation of actin dynamics for phagocytic cup formation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to virus / ruffle membrane / nuclear matrix / cellular response to hydrogen peroxide / protein import into nucleus / actin filament binding / cell-cell junction / cellular response to tumor necrosis factor / Platelet degranulation / actin cytoskeleton / lamellipodium / growth cone / actin cytoskeleton organization / positive regulation of cell growth / vesicle / protein phosphatase binding / dendritic spine / cytoskeleton / hydrolase activity / axon / signaling receptor binding
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site ...ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / 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
Similarity search - Domain/homology
Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesGallus gallus (chicken) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsGalkin VE / Orlova A / Kudryashov DS / Solodukhin A / Reisler E / Schoeder GF / Egelman EH
CitationJournal: Proc Natl Acad Sci U S A / Year: 2011
Title: Remodeling of actin filaments by ADF/cofilin proteins.
Authors: Vitold E Galkin / Albina Orlova / Dmitri S Kudryashov / Alexander Solodukhin / Emil Reisler / Gunnar F Schröder / Edward H Egelman /
Abstract: Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-Å resolution three- ...Cofilin/ADF proteins play key roles in the dynamics of actin, one of the most abundant and highly conserved eukaryotic proteins. We used cryoelectron microscopy to generate a 9-Å resolution three-dimensional reconstruction of cofilin-decorated actin filaments, the highest resolution achieved for a complex of F-actin with an actin-binding protein. We show that the cofilin-induced change in the filament twist is due to a unique conformation of the actin molecule unrelated to any previously observed state. The changes between the actin protomer in naked F-actin and in the actin-cofilin filament are greater than the conformational changes between G- and F-actin. Our results show the structural plasticity of actin, suggest that other actin-binding proteins may also induce large but different conformational changes, and show that F-actin cannot be described by a single molecular model.
History
DepositionNov 23, 2011-
Header (metadata) releaseDec 7, 2011-
Map releaseDec 13, 2011-
UpdateMar 20, 2013-
Current statusMar 20, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.063
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.063
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j0s
  • Surface level: 0.063
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_5354.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the reconstructed volume of the actin-cofilin complex.
Voxel sizeX=Y=Z: 2.5 Å
Density
Contour LevelBy AUTHOR: 0.043 / Movie #1: 0.063
Minimum - Maximum-0.08217396 - 0.23656693
Average (Standard dev.)0.00210833 (±0.02272243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 250.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z250.000250.000250.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.0820.2370.002

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Supplemental data

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Sample components

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Entire : actin decorated with cofilin

EntireName: actin decorated with cofilin
Components
  • Sample: actin decorated with cofilin
  • Protein or peptide: F-Actin
  • Protein or peptide: cofilin-2

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Supramolecule #1000: actin decorated with cofilin

SupramoleculeName: actin decorated with cofilin / type: sample / ID: 1000
Oligomeric state: filament containing one cofilin to one actin
Number unique components: 2

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Macromolecule #1: F-Actin

MacromoleculeName: F-Actin / type: protein_or_peptide / ID: 1 / Name.synonym: F-Actin / Oligomeric state: helical polymer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Gallus gallus (chicken) / synonym: chicken / Tissue: muscle

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Macromolecule #2: cofilin-2

MacromoleculeName: cofilin-2 / type: protein_or_peptide / ID: 2 / Name.synonym: cofilin-2 / Oligomeric state: one cofilin per actin in filament / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Tissue: muscle
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6.35 µm / Number real images: 125 / Bits/pixel: 14
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.3 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 50000
Sample stageSpecimen holder: side entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 162.1 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: SPIDER,IHRSR / Details: map calculated from 13,716 segments
CTF correctionDetails: each EM

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