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- EMDB-1990: Structure of bare F-actin filaments obtained from the same sample... -

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Basic information

Entry
Database: EMDB / ID: EMD-1990
TitleStructure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex
Map dataundecorated F-actin filament
Sample
  • Sample: Bare F-actin filaments
  • Protein or peptide: F-actinActin
KeywordsStructural protein / cytoskeleton / myosin binding / actin binding
Function / homology
Function and homology information


: / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly ...: / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament 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 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: 8.9 Å
AuthorsBehrmann E / Mueller M / Penczek PA / Mannherz HG / Manstein DJ / Raunser S
CitationJournal: Cell / Year: 2012
Title: Structure of the rigor actin-tropomyosin-myosin complex.
Authors: Elmar Behrmann / Mirco Müller / Pawel A Penczek / Hans Georg Mannherz / Dietmar J Manstein / Stefan Raunser /
Abstract: Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions ...Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin.
History
DepositionNov 14, 2011-
Header (metadata) releaseAug 1, 2012-
Map releaseAug 1, 2012-
UpdateAug 1, 2012-
Current statusAug 1, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4a7n
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

image1990.png

Downloads & links

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Map

FileDownload / File: emd_1990.map.gz / Format: CCP4 / Size: 21 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationundecorated F-actin filament
Voxel sizeX=Y=Z: 1.84 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum0.0 - 0.11287101
Average (Standard dev.)0.00048386 (±0.00331855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160220
Spacing160160220
CellA: 294.4 Å / B: 294.4 Å / C: 404.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z160160220
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400404.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160220
D min/max/mean-0.0000.1130.000

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Supplemental data

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Sample components

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Entire : Bare F-actin filaments

EntireName: Bare F-actin filaments
Components
  • Sample: Bare F-actin filaments
  • Protein or peptide: F-actinActin

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Supramolecule #1000: Bare F-actin filaments

SupramoleculeName: Bare F-actin filaments / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: F-actin

MacromoleculeName: F-actin / type: protein_or_peptide / ID: 1 / Name.synonym: actin filament / Number of copies: 14 / Oligomeric state: filament / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / synonym: Rabbit / Tissue: skeletal muscle / Organelle: Sarcoplasm / Location in cell: Sarcoplasm
SequenceGO: GO: 0042643 / InterPro: Actin family

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.2
Details: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine
GridDetails: C-Flat CF-2/1-4C copper 400 mesh
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 101 K / Instrument: GATAN CRYOPLUNGE 3 / Details: Vitrification instrument: Gatan Cryoplunge 3 / Method: Manual blotting for approximately 15 seconds

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 169644 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.1 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 80000
Specialist opticsEnergy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 12.0 eV
Sample stageSpecimen holder: cryogenic stage with side entry access / Specimen holder model: JEOL 3200FSC CRYOHOLDER
TemperatureAverage: 77 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Digitization - Sampling interval: 15.6 µm / Number real images: 836 / Average electron dose: 17 e/Å2
Details: Over 3000 images were taken of which only the best 836 were used for processing
Bits/pixel: 14

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.5 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX
DetailsParticles were selected by hand using e2helixboxer

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Atomic model buiding 1

Initial modelPDB ID:

3mfp

SoftwareName: DireX
DetailsProtocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-4a7n:
Structure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex

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