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- PDB-6vao: Human cofilin-1 decorated actin filament -

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Basic information

Entry
Database: PDB / ID: 6vao
TitleHuman cofilin-1 decorated 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 / neural fold formation / 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 / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization / negative regulation of actin filament bundle assembly / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament depolymerization / positive regulation of synaptic plasticity / actin filament severing / regulation of dendritic spine morphogenesis / host-mediated activation of viral process / establishment of spindle localization / negative regulation of cell adhesion / actin filament depolymerization / negative regulation of cell motility / RHO GTPases Activate ROCKs / negative regulation of cell size / cellular response to interleukin-6 / regulation of cell morphogenesis / cell projection organization / negative regulation of dendritic spine maintenance / positive regulation of cell motility / neural crest cell migration / cytoskeletal motor activator activity / cortical actin cytoskeleton / phosphatidylinositol bisphosphate binding / cellular response to insulin-like growth factor stimulus / myosin heavy chain binding / positive regulation of dendritic spine development / tropomyosin binding / establishment of cell polarity / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / positive regulation of proteolysis / lamellipodium membrane / mitotic cytokinesis / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / Sema3A PAK dependent Axon repulsion / skeletal muscle thin filament assembly / actin monomer binding / positive regulation of focal adhesion assembly / cellular response to interleukin-1 / response to amino acid / postsynaptic density, intracellular component / positive regulation of lamellipodium assembly / Rho protein signal transduction / stress fiber / skeletal muscle fiber development / titin binding / EPHB-mediated forward signaling / actin filament polymerization / cytoskeleton organization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cellular response to epidermal growth factor stimulus / synaptic membrane / response to activity / hippocampus development / actin filament / filopodium / Regulation of actin dynamics for phagocytic cup formation / response to virus / mitochondrial membrane / cellular response to tumor necrosis factor / ruffle membrane / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / nuclear matrix / cellular response to hydrogen peroxide / protein import into nucleus / calcium-dependent protein binding / cell-cell junction / actin filament binding / Platelet degranulation / lamellipodium / actin cytoskeleton / growth cone / actin cytoskeleton organization / positive regulation of cell growth / cell body / protein phosphatase binding / vesicle / dendritic spine / protein domain specific binding / signaling receptor binding / focal adhesion / hydrolase activity / neuronal cell body / calcium ion binding / positive regulation of gene expression
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 / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 ...ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / 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 / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
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 / helical reconstruction / cryo EM / Resolution: 3.4 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
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _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 6, 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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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)305,40520
Polymers303,14710
Non-polymers2,25810
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.: 5 / 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.: 5
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.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of rabbit skeletal actin with human cofilin-1COMPLEX#1-#20MULTIPLE SOURCES
2Actin, alpha skeletal muscleCOMPLEX#11NATURAL
3Cofilin-1COMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Oryctolagus cuniculus (rabbit)9986
22Homo 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
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -162.5 ° / Axial rise/subunit: 27.24 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 1117338
Details: Both bare and cofilin-decorated segments were selected and initially refined together.
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 558272 / Num. of class averages: 1 / Symmetry type: HELICAL

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