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- EMDB-1987: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3) -

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Entry
Database: EMDB / ID: 1987
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3)
KeywordsStructural protein / cytoskeleton / contractile filament / motor activity / myosin binding / actin binding / ATP catabolic process / rigor state
SampleF-actin-myo1E-tropomyosin complex (conformation 3)
SourceOryctolagus cuniculus / mammal / Rabbit / アナウサギ /
Gallus gallus / bird / Chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
Dictyostelium discoideum / fungus / Slime mold /
Map dataConformation 3 of the F-actin-myo1E-tropomyosin complex
Methodhelical reconstruction, at 7.7 A resolution
AuthorsBehrmann E / Mueller M / Penczek PA / Mannherz HG / Manstein DJ / Raunser S
CitationCell, 2012, 150, 327-338

Cell, 2012, 150, 327-338 StrPapers
Structure of the rigor actin-tropomyosin-myosin complex.
Elmar Behrmann / Mirco Müller / Pawel A Penczek / Hans Georg Mannherz / Dietmar J Manstein / Stefan Raunser

DateDeposition: Nov 14, 2011 / Header (metadata) release: Aug 1, 2012 / Map release: Aug 1, 2012 / Last update: Nov 14, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0125
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0125
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4a7f
  • Surface level: 0.0125
  • Imaged by UCSF CHIMERA
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Map

Fileemd_1987.map.gz (map file in CCP4 format, 22001 KB)
Projections & slices
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AxesZ (Sec.)Y (Row.)X (Col.)
220 pix
1.84 A/pix
= 404.8 A
160 pix
1.84 A/pix
= 294.4 A
160 pix
1.84 A/pix
= 294.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.84 A
Density
Contour Level:0.0125 (by author), 0.0125 (movie #1):
Minimum - Maximum0E-8 - 0.07019328
Average (Standard dev.)0.00156007 (0.00584454)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160220
Origin000
Limit159159219
Spacing160160220
CellA: 294.4 A / B: 294.4 A / C: 404.80002 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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-0.0000.0700.002

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Supplemental data

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Sample components

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Entire F-actin-myo1E-tropomyosin complex (conformation 3)

EntireName: F-actin-myo1E-tropomyosin complex (conformation 3) / Details: 7 to 7 to 1 (actin to myosin to tropomyosin) / Number of components: 3 / Oligomeric State: Pentameric

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Component #1: protein, F-actin

ProteinName: F-actin / a.k.a: actin filament / Oligomeric Details: Filament / Number of Copies: 14 / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus / mammal / Rabbit / アナウサギ /
Source (natural)Location in cell: Sarcoplasm / Organ or tissue: Skeletal muscle
External referencesGene Ontology: GO: 0042643 / InterPro: InterPro: 004000

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Component #2: protein, tropomyosin 1 (alpha)

ProteinName: tropomyosin 1 (alpha) / a.k.a: tropomyosin 1 (alpha) / Oligomeric Details: Filament of dimers / Recombinant expression: Yes / Number of Copies: 2
SourceSpecies: Gallus gallus / bird / Chicken / ウズラチャボ, オナガドリ, セキショクヤケイ, トウマル /
Source (engineered)Expression System: Escherichia coli (strain bl21 de3) / bacteria /
Vector: pJC20
Source (natural)Organ or tissue: Gizzard
External referencesInterPro: InterPro: 000533 / Gene Ontology: GO: 0005862

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Component #3: protein, myoE

ProteinName: myoE / a.k.a: myosin 1E / Oligomeric Details: filament / Recombinant expression: Yes / Number of Copies: 14
SourceSpecies: Dictyostelium discoideum / fungus / Slime mold / / Strain: AX2
Source (engineered)Expression System: Dictyostelium discoideum / fungus / / Vector: pDXA-3H
External referencesGene Ontology: GO: 0045160 / InterPro: InterPro: 001609

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED / Delta z: 27.6 A / Delta phi: 166.5 deg.
Sample solutionSpecimen conc.: 0.01 mg/ml
Buffer solution: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine
pH: 7.2
Support filmC-Flat CF-2/1-4C copper 400 mesh
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 90 % / Method: Manual blotting for approximately 15 seconds / Details: Vitrification instrument: Gatan Cryoplunge 3

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal), 169644 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification
Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 750 - 1500 nm / Energy filter: in-column Omega filter / Energy window: 0-12 eV
Specimen HolderHolder: cryogenic stage with side entry access / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 77 K
CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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Image acquisition

Image acquisitionNumber of digital images: 836 / Sampling size: 15.6 microns / Bit depth: 14
Details: Over 3000 images were taken of which only the best 836 were used for processing

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Image processing

ProcessingMethod: helical reconstruction / Details: Particles were selected by hand using e2helixboxer
3D reconstructionAlgorithm: IHRSR / Software: SPARX / CTF correction: each particle / Details: Particles were classified using CODIM / Resolution: 7.7 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: DireX / Refinement protocol: flexible / Refinement space: REAL
Details: Protocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera
Input PDB model: 1LKX
Chain ID: 1LKX_C
Output model

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