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- EMDB-1872: Actin filament pointed end -

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Basic information

Entry
Database: EMDB / ID: EMD-1872
TitleActin filament pointed end
Map dataThis is a volume map of the actin filament pointed end
Sample
  • Sample: Rabbit skeletal actin
  • Protein or peptide: Actin, alpha skeletal muscle
Keywordsactin / actin filament / cytoskeleton / cell motility
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 / skeletal muscle fiber development / stress fiber / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.9 Å
AuthorsNarita A / Oda T / Maeda Y
CitationJournal: EMBO J / Year: 2011
Title: Structural basis for the slow dynamics of the actin filament pointed end.
Authors: Akihiro Narita / Toshiro Oda / Yuichiro Maéda /
Abstract: The actin filament has clear polarity where one end, the pointed end, has a much slower polymerization and depolymerization rate than the other end, the barbed end. This intrinsic difference of the ...The actin filament has clear polarity where one end, the pointed end, has a much slower polymerization and depolymerization rate than the other end, the barbed end. This intrinsic difference of the ends significantly affects all actin dynamics in the cell, which has central roles in a wide spectrum of cellular functions. The detailed mechanism underlying this difference has remained elusive, because high-resolution structures of the filament ends have not been available. Here, we present the structure of the actin filament pointed end obtained using a single particle analysis of cryo-electron micrographs. We determined that the terminal pointed end subunit is tilted towards the penultimate subunit, allowing specific and extra loop-to-loop inter-strand contacts between the two end subunits, which is not possible in other parts of the filament. These specific contacts prevent the end subunit from dissociating. For elongation, the loop-to-loop contacts also inhibit the incorporation of another actin monomer at the pointed end. These observations are likely to account for the less dynamic pointed end.
History
DepositionFeb 2, 2011-
Header (metadata) releaseFeb 9, 2011-
Map releaseMar 25, 2011-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.61
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.61
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2y83
  • Surface level: 4.61
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1872.jpg

Downloads & links

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Map

FileDownload / File: emd_1872.map.gz / Format: CCP4 / Size: 355.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume map of the actin filament pointed end
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.41 Å/pix.
x 58 pix.
= 197.925 Å		3.41 Å/pix.
x 40 pix.
= 136.5 Å		3.41 Å/pix.
x 40 pix.
= 136.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.4125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.61 / Movie #1: 4.61
Minimum - Maximum-11.912599999999999 - 16.473800000000001
Average (Standard dev.)0.224494 (±3.23024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions404058
Spacing404058
CellA: 136.5 Å / B: 136.5 Å / C: 197.925 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.41253.41253.4125
M x/y/z404058
origin x/y/z0.0000.0000.000
length x/y/z136.500136.500197.925
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS404058
D min/max/mean-11.91316.4740.224

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Supplemental data

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Sample components

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Entire : Rabbit skeletal actin

EntireName: Rabbit skeletal actin
Components
  • Sample: Rabbit skeletal actin
  • Protein or peptide: Actin, alpha skeletal muscle

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Supramolecule #1000: Rabbit skeletal actin

SupramoleculeName: Rabbit skeletal actin / type: sample / ID: 1000 / Oligomeric state: Helical multimer / Number unique components: 1

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Name.synonym: Actin / Oligomeric state: Helical multimer / Recombinant expression: No
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: Skeletal muscle

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.4
Details: 50 mM NaCl, 10 mM sodium phosphate buffer (pH 7.4), 3 mM MgCl2, 0.005% (w/v) NaN3, 0.7 mM DTT
GridDetails: quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 4 K / Instrument: OTHER / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FSC
TemperatureAverage: 4 K
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 142 / Average electron dose: 34 e/Å2 / Bits/pixel: 12
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: Jeol liquid helium stage / Specimen holder model: JEOL

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EOS / Number images used: 714
Final two d classificationNumber classes: 72

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Atomic model buiding 1

Initial modelPDB ID:

2zwh


Chain - Chain ID: A
SoftwareName: EOS
DetailsProtocol: Rigid body and molecular dynamics. Molecular dynamics simulation after rigid body fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-2y83:
Actin filament pointed end

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