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- EMDB-20719: Bare actin from partially cofilin-decorated actin filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-20719
TitleBare actin from partially cofilin-decorated actin filaments
Map dataUnmasked final map of bare actin from partially cofilin-decorated actin filaments. This map was sharpened with a B-factor of -235.
Sample
  • Complex: Complex of rabbit skeletal actin with human cofilin-1
    • Complex: Rabbit Skeletal Actin
      • Protein or peptide: Rabbit skeletal actin
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / stress fiber / skeletal muscle fiber development / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
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
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 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 SciencesGM097348 United States
National Institutes of Health/National Institute of General Medical SciencesGM110533001 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-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
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  • Surface view with fitted model
  • Atomic models: PDB-6vau
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vau
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20719.png

Downloads & links

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Map

FileDownload / File: emd_20719.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnmasked final map of bare actin from partially cofilin-decorated actin filaments. This map was sharpened with a B-factor of -235.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 220 pix.
= 293.04 Å		1.33 Å/pix.
x 220 pix.
= 293.04 Å		1.33 Å/pix.
x 220 pix.
= 293.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.34932137 - 0.56992716
Average (Standard dev.)0.0008793467 (±0.01907336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 293.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3321.3321.332
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z293.040293.040293.040
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ172172172
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.3490.5700.001

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Supplemental data

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Mask #1

Fileemd_20719_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Symmetrized half map (1/2) of bare actin from...

Fileemd_20719_half_map_1.map
AnnotationSymmetrized half map (1/2) of bare actin from partially cofilin-decorated actin filaments.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Symmetrized half map (2/2) of bare actin from...

Fileemd_20719_half_map_2.map
AnnotationSymmetrized half map (2/2) of bare actin from partially cofilin-decorated actin filaments.
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 rabbit skeletal actin with human cofilin-1

EntireName: Complex of rabbit skeletal actin with human cofilin-1
Components
  • Complex: Complex of rabbit skeletal actin with human cofilin-1
    • Complex: Rabbit Skeletal Actin
      • Protein or peptide: Rabbit skeletal actin

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Supramolecule #1: Complex of rabbit skeletal actin with human cofilin-1

SupramoleculeName: Complex of rabbit skeletal actin with human cofilin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Rabbit Skeletal Actin

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

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Macromolecule #1: Rabbit skeletal actin

MacromoleculeName: Rabbit skeletal actin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTL KYPIEHGIIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE K MTQIMFET FNVPAMYVAI QAVLSLYASG RTTGIVLDSG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTL KYPIEHGIIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE K MTQIMFET FNVPAMYVAI QAVLSLYASG RTTGIVLDSG DGVTHNVPIY EGYALPHAIM RL DLAGRDL TDYLMKILTE RGYSFVTTAE REIVRDIKEK LCYVALDFEN EMATAASSSS LEK SYELPD GQVITIGNER FRCPETLFQP SFIGMESAGI HETTYNSIMK CDIDIRKDLY ANNV MSGGT TMYPGIADRM QKEITALAPS TMKIKIIAPP ERKYSVWIGG SILASLSTFQ QMWIT KQEY DEAGPSIVHR KCF

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.6
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 27.42 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.63 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 559067
Segment selectionNumber selected: 1117338
Details: Both bare and cofilin-decorated segments were selected and initially refined together
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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