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- PDB-6uby: Isolated cofilin bound to an actin filament -

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Basic information

Entry
Database: PDB / ID: 6uby
TitleIsolated cofilin bound to an actin filament
Components
  • Actin, alpha skeletal muscle
  • Cofilin-1
KeywordsSTRUCTURAL PROTEIN / Cytoskeleton
Function / homology
Function and homology information


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 / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / actin filament severing activity / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation ...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 / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / actin filament severing activity / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / negative regulation of actin filament bundle assembly / positive regulation of actin filament depolymerization / modification of postsynaptic actin cytoskeleton / positive regulation of embryonic development / positive regulation of cell motility / negative regulation of actin filament depolymerization / actin filament severing / host-mediated activation of viral process / negative regulation of cell adhesion / positive regulation of synaptic plasticity / establishment of spindle localization / regulation of dendritic spine morphogenesis / negative regulation of cell motility / actin filament depolymerization / RHO GTPases Activate ROCKs / cellular response to interleukin-6 / negative regulation of dendritic spine maintenance / cellular response to insulin-like growth factor stimulus / cytoskeletal motor activator activity / positive regulation of dendritic spine development / cortical actin cytoskeleton / phosphatidylinositol bisphosphate binding / myosin heavy chain binding / tropomyosin binding / actin filament bundle / positive regulation of proteolysis / troponin I binding / filamentous actin / mesenchyme migration / lamellipodium membrane / mitotic cytokinesis / cellular response to interleukin-1 / skeletal muscle myofibril / Sema3A PAK dependent Axon repulsion / striated muscle thin filament / actin filament bundle assembly / skeletal muscle thin filament assembly / Rho protein signal transduction / actin monomer binding / positive regulation of focal adhesion assembly / positive regulation of lamellipodium assembly / postsynaptic density, intracellular component / skeletal muscle fiber development / actin filament polymerization / stress fiber / titin binding / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cellular response to epidermal growth factor stimulus / response to activity / protein import into nucleus / hippocampus development / cellular response to tumor necrosis factor / filopodium / actin filament / synaptic membrane / Regulation of actin dynamics for phagocytic cup formation / response to virus / cellular response to hydrogen peroxide / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ruffle membrane / nuclear matrix / mitochondrial membrane / calcium-dependent protein binding / actin filament binding / actin cytoskeleton organization / cell-cell junction / Platelet degranulation / positive regulation of cell growth / lamellipodium / growth cone / cell body / protein phosphatase binding / dendritic spine / vesicle / hydrolase activity / protein domain specific binding / signaling receptor binding / focal adhesion / neuronal cell body / positive regulation of gene expression / calcium ion binding / negative regulation of apoptotic process / glutamatergic synapse / magnesium ion binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein 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
ADENOSINE-5'-DIPHOSPHATE / Cofilin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsHuehn, A.R. / Bibeau, J.P. / Schramm, A.C. / Cao, W. / De La Cruz, E.M. / Sindelar, C.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097348 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110533001 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structures of cofilin-induced structural changes reveal local and asymmetric perturbations of actin filaments.
Authors: Andrew R Huehn / Jeffrey P Bibeau / Anthony C Schramm / Wenxiang Cao / Enrique M De La Cruz / Charles V Sindelar /
Abstract: Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with ...Members of the cofilin/ADF family of proteins sever actin filaments, increasing the number of filament ends available for polymerization or depolymerization. Cofilin binds actin filaments with positive cooperativity, forming clusters of contiguously bound cofilin along the filament lattice. Filament severing occurs preferentially at boundaries between bare and cofilin-decorated (cofilactin) segments and is biased at 1 side of a cluster. A molecular understanding of cooperative binding and filament severing has been impeded by a lack of structural data describing boundaries. Here, we apply methods for analyzing filament cryo-electron microscopy (cryo-EM) data at the single subunit level to directly investigate the structure of boundaries within partially decorated cofilactin filaments. Subnanometer resolution maps of isolated, bound cofilin molecules and an actin-cofilactin boundary indicate that cofilin-induced actin conformational changes are local and limited to subunits directly contacting bound cofilin. An isolated, bound cofilin compromises longitudinal filament contacts of 1 protofilament, consistent with a single cofilin having filament-severing activity. An individual, bound phosphomimetic (S3D) cofilin with weak severing activity adopts a unique binding mode that does not perturb actin structure. Cofilin clusters disrupt both protofilaments, consistent with a higher severing activity at boundaries compared to single cofilin. Comparison of these structures indicates that this disruption is substantially greater at pointed end sides of cofilactin clusters than at the barbed end. These structures, with the distribution of bound cofilin clusters, suggest that maximum binding cooperativity is achieved when 2 cofilins occupy adjacent sites. These results reveal the structural origins of cooperative cofilin binding and actin filament severing.
History
DepositionSep 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 20, 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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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Cofilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,46923
Polymers355,3089
Non-polymers3,16114
Water00
1


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

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Components

#1: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42096.953 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18532.531 Da / Num. of mol.: 1
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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Compound detailsThe major close contacts arise because the authors have fitted rigid-body atomic models into low ...The major close contacts arise because the authors have fitted rigid-body atomic models into low resolution maps
Has ligand of interestN
Sequence detailsThe molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt ...The molecules in the experiments were: Rabbit actin (UniProt P68135) and Human cofilin-1 (UniProt P23528), however the sequences modeled in the coordinates correspond to the sequences from Chicken actin and Chicken cofilin-2 since those were pdb models of homolog molecules used to fit into the cryo-EM density maps.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of rabbit skeletal actin with isolated, bound human cofilin-1COMPLEX#1-#20MULTIPLE SOURCES
2Rabbit Skeletal ActinCOMPLEX#11NATURAL
3Human Cofilin-1COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Oryctolagus cuniculus (rabbit)9986
33Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: UCSF Chimera / Category: model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1117338
Details: Both bare and cofilin-decorated segments were selected and initially refined together.
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8917
Details: Filament segments with isolated, bound cofilin were split into even and odd halves for FSC calculations.
Symmetry type: POINT
Atomic model building

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

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
16DJO

6djo

B6DJO14-375
25YU8

5yu8

I5YU823-166

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