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- EMDB-20724: Isolated S3D-cofilin bound to an actin filament -

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Basic information

Entry
Database: EMDB / ID: EMD-20724
TitleIsolated S3D-cofilin bound to an actin filament
Map dataFinal unmasked map of isolated S3D-cofilin bound to an actin filament. This map was sharpened with a B-factor of -250.
Sample
  • Complex: Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal actin filaments
    • Complex: Rabbit Skeletal Actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Human S3D-Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / lamellipodium membrane / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / mitotic cytokinesis / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / cytoskeleton organization / EPHB-mediated forward signaling / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / growth cone / cell body / actin cytoskeleton organization / vesicle / hydrolase activity / protein domain specific binding / focal adhesion / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / magnesium ion binding / extracellular space / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / 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, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsHuehn AR / Bibeau JP / Schramm AC / Cao W / De La Cruz EM / Sindelar CV
Funding support United States, 2 items
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, 2019-
Header (metadata) releaseJan 1, 2020-
Map releaseJan 1, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uc0
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6uc0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20724.png

Downloads & links

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Map

FileDownload / File: emd_20724.map.gz / Format: CCP4 / Size: 226.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal unmasked map of isolated S3D-cofilin bound to an actin filament. This map was sharpened with a B-factor of -250.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 390 pix.
= 486.33 Å		1.25 Å/pix.
x 390 pix.
= 486.33 Å		1.25 Å/pix.
x 390 pix.
= 486.33 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.247 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165 / Movie #1: 0.0165
Minimum - Maximum-0.007820488 - 0.044876464
Average (Standard dev.)-0.00002487521 (±0.0019669393)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions390390390
Spacing390390390
CellA=B=C: 486.33 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2471.2471.247
M x/y/z390390390
origin x/y/z0.0000.0000.000
length x/y/z486.330486.330486.330
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ720720720
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS390390390
D min/max/mean-0.0080.045-0.000

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Supplemental data

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Mask #1

Fileemd_20724_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (1/2) of isolated S3D-cofilin bound to an actin filament.

Fileemd_20724_half_map_1.map
AnnotationHalf map (1/2) of isolated S3D-cofilin bound to an actin filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map (2/2) of isolated S3D-cofilin bound to an actin filament.

Fileemd_20724_half_map_2.map
AnnotationHalf map (2/2) of isolated S3D-cofilin bound to an actin filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal ...

EntireName: Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal actin filaments
Components
  • Complex: Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal actin filaments
    • Complex: Rabbit Skeletal Actin
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Human S3D-Cofilin-1
      • Protein or peptide: Cofilin-1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal ...

SupramoleculeName: Complex of isolated human S3D-cofilin-1 bound to rabbit skeletal actin filaments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Rabbit Skeletal Actin

SupramoleculeName: Rabbit Skeletal Actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Human S3D-Cofilin-1

SupramoleculeName: Human S3D-Cofilin-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Point mutation at S3D
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Cofilin-1

MacromoleculeName: Cofilin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.560541 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADGVAVSDG VIKVFNDMKV RKSSTPEEVK KRKKAVLFCL SEDKKNIILE EGKEILVGDV GQTVDDPYAT FVKMLPDKDC RYALYDATY ETKESKKEDL VFIFWAPESA PLKSKMIYAS SKDAIKKKLT GIKHELQANC YEEVKDRCTL AEKLGGSAVI S LEGKPL

UniProtKB: Cofilin-1

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 7 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 217500
Details: Both bare and S3D-cofilin-decorated filament segments were selected and initially refined together.
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Segments with isolated, bound S3D-cofilin were split into even and odd halves for FSC calculations.
Number images used: 20082
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 8 / Avg.num./class: 27500
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6djo

chain_id: B, residue_range: 4-375, source_name: PDB, initial_model_type: experimental model

5yu8

chain_id: I, residue_range: 3-166, source_name: PDB, initial_model_type: experimental model
Output model

PDB-6uc0:
Isolated S3D-cofilin bound to an actin filament

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