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

by helical reconstruction, at 7.7 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.0125, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0125, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a7f, Surface level: 0.0125, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4a7f, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1987
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 3)
MapConformation 3 of the F-actin-myo1E-tropomyosin complex
SampleF-actin-myo1E-tropomyosin complex (conformation 3)
KeywordsStructural protein, cytoskeleton, contractile filament, motor activity, myosin binding, actin binding, ATP catabolic process, rigor state
AuthorsBehrmann E, Mueller M, Penczek PA, Mannherz HG, Manstein DJ, Raunser S
DateDeposition: 2011-11-14, Header release: 2012-08-01, Map release: 2012-08-01, Last update: 2012-08-01
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.0125, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 0.0125, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-4a7f, Surface level: 0.0125, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-4a7f, Image by Jmol

Supplemental images
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Related Structure Data
Related Entries

PDB-4a7f

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Article
Citation - Primary
ArticleCell, Vol. 150, Issue 2, Page 327-38, Year 2012
TitleStructure of the rigor actin-tropomyosin-myosin complex.
AuthorsElmar Behrmann, Mirco Müller, Pawel A Penczek, Hans Georg Mannherz, Dietmar J Manstein, Stefan Raunser
Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
KeywordsActins (chemistry), Animals, Cryoelectron Microscopy, Humans, Models, Molecular, Multiprotein Complexes (chemistry), Muscle, Skeletal (metabolism), Muscular Diseases (genetics), Myosins (chemistry, 3.6.4.1), Rabbits, Tropomyosin (chemistry)
LinksPII: S0092-8674(12)00707-6, DOI: 10.1016/j.cell.2012.05.037, PubMed: 22817895, PMC: PMC4163373
Map
Fileemd_1987.map.gz ( map file in CCP4 format, 22001 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:0.0125 (by author), 0.0125 (movie #1):
Minimum - Maximum: 0E-8 - 0.07019328
Average (Standard dev.): 0.00156007 (0.00584454)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160220
Origin000
Limit159159219
Spacing160160220
Unit CellA: 294.4 A, B: 294.4 A, C: 404.80002 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.84 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.0000.0700.002
Annotation DetailsConformation 3 of the F-actin-myo1E-tropomyosin complex
Supplement
Images
Images
Sample
NameF-actin-myo1E-tropomyosin complex (conformation 3)
Number of Components3
Oligomeric StatePentameric
Details7 to 7 to 1 (actin to myosin to tropomyosin)
Component #1: protein - actin filament
Scientific nameF-actin
Common Nameactin filament
Oligomeric DetailsFilament
Number of Copies14
Scientific Name of SpeciesOryctolagus cuniculus

Common Name of SpeciesRabbit
NCBI taxonomy9986
Recombinant expressionNo
Natural SourceCell Location: Sarcoplasm
Organ Or Tissue: Skeletal muscle
LinksGene Ontology: GO:0042643, Inter Pro: IPR:004000
Component #2: protein - tropomyosin 1 (alpha)
Scientific nametropomyosin 1 (alpha)
Oligomeric DetailsFilament of dimers
Number of Copies2
Scientific Name of SpeciesGallus gallus

Common Name of SpeciesChicken
NCBI taxonomy9031
Recombinant expressionYes
Natural SourceOrgan Or Tissue: Gizzard
Engineered SourceVector: pJC20
Expression system: Escherichia coli (strain BL21 DE3)
LinksInter Pro: IPR:000533, Gene Ontology: GO:0005862
Component #3: protein - myosin 1E
Scientific namemyoE
Common Namemyosin 1E
Oligomeric Detailsfilament
Number of Copies14
Scientific Name of SpeciesDictyostelium discoideum

Common Name of SpeciesSlime mold
NCBI taxonomy44689
StrainAX2
Recombinant expressionYes
Engineered SourceVector: pDXA-3H
NCBI taxonomy: 44689
Expression system: Dictyostelium discoideum
LinksGene Ontology: GO:0045160, Inter Pro: IPR:001609
Experiment
Sample Preparation
Helical ParametersDelta Z: 27.6 A
Delta Phi: 166.5 degrees
Hand: LEFT HANDED
Specimen Conc0.01 mg/ml
Specimen Support DetailsC-Flat CF-2/1-4C copper 400 mesh
Specimen Statefilament
BufferpH: 7.2
Details: 5mM Tris, 100mM KCl, 2mM MgCl2, 50mM glutamine, 50mM arginine
Vitrification
MethodManual blotting for approximately 15 seconds
Cryogen NameETHANE
DetailsVitrification instrument: Gatan Cryoplunge 3
Humidity90
InstrumentGATAN CRYOPLUNGE 3
Temperature101 Kelvin
Imaging
MicroscopeJEOL 3200FSC
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose17 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000, Calibrated: 169644
Astigmatismobjective lens astigmatism was corrected at 150,000 times magnification
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus750 nm - 1500 nm
Energy FilterEnergy Filter: in-column Omega filter , Energy Window: 0-12 eV
Specimen Holder
Holdercryogenic stage with side entry access
ModelJEOL 3200FSC CRYOHOLDER
Temperature77 K
Camera
DetectorTVIPS TEMCAM-F816 (8k x 8k)
Image Acquisition
Number of Digital Images836
Sampling Size15.6
Quant Bit Number14
DetailsOver 3000 images were taken of which only the best 836 were used for processing
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmIHRSR
SoftwareSPARX
CTF Correctioneach particle
DetailsParticles were classified using CODIM
Resolution By Author7.7 A
Resolution MethodFSC 0.5
Helical
DetailsParticles were selected by hand using e2helixboxer
Atomic Model Fitting
Model #0
DetailsProtocol: geometry-based conformational sampling using Deformable Elastic Network (DEN) approach. Initial placement was performed using rigid-body fitting in Chimera
SoftwareDireX
Refinement Protocolflexible
Refinement SpaceREAL
PDB Entry ID1LKX
PDB Chain ID1LKX_C
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1987.xml (10.7 KB)
Map dataemd_1987.map.gz (4.9 MB)
Imagesimage1987.png (91.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1987
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.9 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 6.6 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB