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- PDB-3j0s: Remodeling of actin filaments by ADF cofilin proteins -

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Basic information

Entry
Database: PDB / ID: 3j0s
TitleRemodeling of actin filaments by ADF cofilin proteins
Components
  • Actin, cytoplasmic 1
  • Cofilin-2
KeywordsCONTRACTILE PROTEIN/PROTEIN BINDING / helical polymer / CONTRACTILE PROTEIN-ACTIN BINDING PROTEIN complex / CONTRACTILE PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / RHO GTPases activate IQGAPs / UCH proteinases / DNA Damage Recognition in GG-NER / Adherens junctions interactions / Clathrin-mediated endocytosis / RHO GTPases Activate Formins / actin filament fragmentation / positive regulation of embryonic development ...Gap junction degradation / Formation of annular gap junctions / RHO GTPases activate IQGAPs / UCH proteinases / DNA Damage Recognition in GG-NER / Adherens junctions interactions / Clathrin-mediated endocytosis / RHO GTPases Activate Formins / actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / structural constituent of postsynaptic actin cytoskeleton / positive regulation by host of viral process / EPH-ephrin mediated repulsion of cells / dense body / actin filament severing / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / regulation of dendritic spine morphogenesis / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / NuA4 histone acetyltransferase complex / lamellipodium membrane / mitotic cytokinesis / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / cytoskeleton organization / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / axonogenesis / cell motility / actin filament / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / growth cone / actin cytoskeleton organization / vesicle / cytoskeleton / axon / focal adhesion / synapse / negative regulation of apoptotic process / protein kinase binding / extracellular space / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 9 Å
AuthorsGalkin, V.E. / Orlova, A. / Kudryashov, D.S. / Solodukhin, A. / Reisler, E. / Schroeder, G.F. / Egelman, E.H.
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 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jun 6, 2012Group: Database references
Revision 1.3Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Actin, cytoplasmic 1
B: Actin, cytoplasmic 1
C: Actin, cytoplasmic 1
D: Actin, cytoplasmic 1
E: Actin, cytoplasmic 1
F: Actin, cytoplasmic 1
G: Actin, cytoplasmic 1
H: Actin, cytoplasmic 1
I: Actin, cytoplasmic 1
J: Actin, cytoplasmic 1
K: Actin, cytoplasmic 1
L: Actin, cytoplasmic 1
M: Cofilin-2
O: Cofilin-2
N: Cofilin-2
Q: Cofilin-2
P: Cofilin-2
S: Cofilin-2
R: Cofilin-2
U: Cofilin-2
T: Cofilin-2
W: Cofilin-2
V: Cofilin-2
X: Cofilin-2


Theoretical massNumber of molelcules
Total (without water)722,20824
Polymers722,20824
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -162.1 DEGREES; RISE PER SUBUNIT (HEIGHT) = 27.6 ANGSTROM

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Components

#1: Protein
Actin, cytoplasmic 1 / / Beta-actin


Mass: 41651.465 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: muscleSkeletal muscle / References: UniProt: P60706
#2: Protein
Cofilin-2 / / Cofilin / muscle isoform


Mass: 18532.531 Da / Num. of mol.: 12 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli (E. coli) / References: UniProt: P23528*PLUS
Sequence detailsTHE AUTHORS STATE THAT HUMAN COFILIN-2 WAS USED IN THE EXPERIMENT, BUT HUMAN COFILIN-1 (UNP P23528) ...THE AUTHORS STATE THAT HUMAN COFILIN-2 WAS USED IN THE EXPERIMENT, BUT HUMAN COFILIN-1 (UNP P23528) WAS USED FOR MODELING.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: actin decorated with cofilin / Type: COMPLEX / Details: filament containing one cofilin to one actin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 5300 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: SIDE ENTRY
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 125

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Processing

Software
NameClassification
SPIDERrefinement
IHRSRrefinement
EM software
IDNameCategory
1IHRSR3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: each EM
Helical symmertyAngular rotation/subunit: 162.1 ° / Axial rise/subunit: 27.6 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 9 Å / Resolution method: FSC / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms50556 0 0 0 50556

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