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Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)

by helical reconstruction, at 7.8 A resolution

Movie

Orientation:

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1988, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1988, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 4a7h
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)
DescriptorACTIN
ALPHA SKELETAL MUSCLE
TROPOMYOSIN 1-ALPHA CHAIN
MYOSIN IE HEAVY CHAIN (E.C.3.6.4.1)
KeywordsSTRUCTURAL PROTEIN/HYDROLASE, STRUCTURAL PROTEIN-HYDROLASE COMPLEX, STRUCTURAL PROTEIN, CYTOSKELETON, CONTRACTILE FILAMENT, MOTOR ACTIVITY, MYOSIN BINDING, ACTIN BINDING, ATP CATABOLIC PROCESS, RIGOR STATE
AuthorsBehrmann, E., Mueller, M., Penczek, P.A., Mannherz, H.G., Manstein, D.J., Raunser, S.
DateDeposition: 2011-11-14, Release: 2012-08-01
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Compound detailsENGINEERED RESIDUE IN CHAIN C, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN I, SER 334 TO GLU ENGINEERED RESIDUE IN CHAIN J, SER 334 TO GLU
Sequence detailsSEQUENCE IS NOT BASED ON THE EXPERIMENTAL PROTEIN AS NO FULL-LENGTH TROPOMYOSIN STRUCTURES WERE AVAILABLE, BUT ON A MODEL OBTAINED FROM MD SIMULATIONS DESCRIBED IN LI, X. E. ET AL. TROPOMYOSIN POSITION ON F-ACTIN REVEALED BY EM RECONSTRUCTION AND COMPUTATIONAL CHEMISTRY. BIOPHYS J 100, 1005-1013, (2011) SEQUENCE AS DESCRIBED BY KOLLMAR, M., DURRWANG, U., KLICHE, W., MANSTEIN, D. J. & KULL, F. J. CRYSTAL STRUCTURE OF THE MOTOR DOMAIN OF A CLASS-I MYOSIN. EMBO J 21, 2517-2525, (2002).
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1988, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1988, Image by UCSF CHIMERA

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EMDB-1988

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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
Components
ID 1 : F-ACTIN, ALPHA-ACTIN-1
Image
DescriptionACTIN, ALPHA SKELETAL MUSCLE
Typepolypeptide(L)
Formula weight41875.984 Da
Number of molecules5
ID1
SourceMethod: Isolated from a natural source
Common name: RABBIT
NCBI taxonomy: ID:9986
Organ: SARCOPLASM
Organism scientific: ORYCTOLAGUS CUNICULUS


Tissue: SKELETAL MUSCLE
LinksUniProt: P68135, Sequence view
ID 2 : TROPOMYOSIN 1-ALPHA CHAIN
Image
DescriptionTROPOMYOSIN 1-ALPHA CHAIN
Typepolypeptide(L)
FragmentRESIDUES 98-233
Formula weight15807.776 Da
Number of molecules2
ID2
SourceMethod: Isolated from a genetically manipulated source
Gene: RABBIT, GIZZARD, ID:9986, ORYCTOLAGUS CUNICULUS
Host: ID:469008, ESCHERICHIA COLI

, BL21(DE3)
Plasmid name: PJC20
LinksUniProt: P58772, Sequence view
ID 3 : MYOE
Image
DescriptionMYOSIN IE HEAVY CHAIN
Typepolypeptide(L)
FragmentRESIDUES 1-697
MutationYES
Formula weight79207.945 Da
Number of molecules3
ID3
Ec3.6.4.1
SourceMethod: Isolated from a genetically manipulated source
Gene: SLIME MOLD, AX2, ID:44689, DICTYOSTELIUM DISCOIDEUM
Host: ID:44689, DICTYOSTELIUM DISCOIDEUM


Plasmid name: PDXA-3H
LinksUniProt: Q03479, Sequence view
ID 4 : ADENOSINE-5'-DIPHOSPHATE
Image
DescriptionADENOSINE-5'-DIPHOSPHATE
Typenon-polymer
Formula weight427.203 Da
Number of molecules5
ID4
SourceMethod: Obtained synthetically
ID 5 : CALCIUM ION
Image
DescriptionCALCIUM ION
Typenon-polymer
Formula weight40.080 Da
Number of molecules5
ID5
SourceMethod: Obtained synthetically
Sample
Assembly
Aggregation stateFILAMENT
DetailsCMOS IMAGE FRAMES SELECTED BY POWER SPECTRUM
NameF-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 2)
Buffer
Name5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE CRYO EM
Sample preparation
pH7.2
Sample concentration0.01 mg/ml
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: OTHER
DetailsBEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage200 kV
Electron dose1.7 e/A**2
Illumination modeLOW DOSE FLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 169644 X, Nominal: 80000 X
CsNominal: 4.1 mm
Nominal defocusMax: 1500 nm, Min: 750 nm
Specimen holder
Temperature77 Kelvin
Detector
TypeTEMCAM-F816
Image scans
Number digital images836
Processing
2D projection selection
Number of particles9650
Software nameSPARX
3D reconstruction
Actual pixel size1.84 A/pix
CTF correction methodEACH PARTICLE
DetailsSUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1988 (DEPOSITION ID: 10379).
MethodIHRSR
Nominal pixel size1.84 A/pix
Resolution7.8 A
3D fitting
MethodGEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH
Refinement ProtocolEM
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID3MFP;1LKX
Refine
Refine idELECTRON MICROSCOPY
Ls d res high7.80 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high7.80
Total atoms33500
Ligand atoms140
Protein atoms33360
Download
PDB format
Allpdb4a7h.ent.gz
pdb4a7h.ent (uncompressed file)
Header onlypdb4a7h.ent.gz
mmCIF format
mmCIF4a7h.cif.gz
XML format
All4a7h.xml.gz
No-atom4a7h-noatom.xml.gz
Ext-atom4a7h-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.7 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5 MB