PDB-4a7h: Structure of the Actin-Tropomyosin-Myosin Complex (rigo...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 4a7h
Title	Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)
Descriptor	ACTIN ALPHA SKELETAL MUSCLE TROPOMYOSIN 1-ALPHA CHAIN MYOSIN IE HEAVY CHAIN (E.C.3.6.4.1)
Keywords	STRUCTURAL PROTEIN/HYDROLASE, STRUCTURAL PROTEIN-HYDROLASE COMPLEX, STRUCTURAL PROTEIN, CYTOSKELETON, CONTRACTILE FILAMENT, MOTOR ACTIVITY, MYOSIN BINDING, ACTIN BINDING, ATP CATABOLIC PROCESS, RIGOR STATE
Authors	Behrmann, E., Mueller, M., Penczek, P.A., Mannherz, H.G., Manstein, D.J., Raunser, S.
Date	Deposition: 2011-11-14, Release: 2012-08-01
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Compound details	ENGINEERED 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 details	SEQUENCE 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
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1988, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1988, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1988 CiteFit EMDB-1987 Cite EMDB-1989 Cite EMDB-1990 Cite PDB-4a7f Cite PDB-4a7l Cite PDB-4a7n Cite PDB-1alm PDB-1atn PDB-1eqy PDB-1esv PDB-1h1v PDB-1ijj PDB-1j6z PDB-1kxp PDB-1lcu PDB-1lkx PDB-1lot PDB-1m8q PDB-1ma9 PDB-1mvw PDB-1nwk PDB-1o18 PDB-1o19 PDB-1o1a PDB-1o1b PDB-1o1c PDB-1o1d PDB-1o1e PDB-1o1f PDB-1o1g PDB-1p8z PDB-1qz5 PDB-1qz6 PDB-1rdw PDB-1rfq PDB-1rgi PDB-1s22 PDB-1sqk PDB-1t44 PDB-1uy5 PDB-1wua PDB-1y64 PDB-2a3z PDB-2a40 PDB-2a41 PDB-2a42 PDB-2a5x PDB-2asm PDB-2aso PDB-2asp PDB-2d1k PDB-2d3e PDB-2ff3 PDB-2ff6 PDB-2fxu PDB-2tma PDB-2v51 PDB-2v52 PDB-2vcp PDB-2vyp PDB-2w49 PDB-2w4u PDB-2y83 PDB-2yje PDB-2yjf Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-4a7f PDB-4a7l EMDB-5163 PDB-3bbn PDB-3iy8 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell, Vol. 150, Issue 2, Page 327-38, 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 Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
Keywords	Actins (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)
Links	PII: S0092-8674(12)00707-6, DOI: 10.1016/j.cell.2012.05.037, PubMed: 22817895

Components
ID 1 : F-ACTIN, ALPHA-ACTIN-1
Image
Description	ACTIN, ALPHA SKELETAL MUSCLE
Type	polymer
Formula weight	41875.984 Da
Number of molecules	5
Source	Method: Isolated from a natural source Common name: RABBIT NCBI taxonomy: ID:9986 Organ: SARCOPLASM Organism scientific: ORYCTOLAGUS CUNICULUS Tissue: SKELETAL MUSCLE
Links	UniProt: P68135, Sequence view
ID 2 : TROPOMYOSIN 1-ALPHA CHAIN
Image
Description	TROPOMYOSIN 1-ALPHA CHAIN
Type	polymer
Fragment	RESIDUES 98-233
Formula weight	15807.776 Da
Number of molecules	2
Source	Method: Isolated from a genetically manipulated source Gene: RABBIT, GIZZARD, ID:9986, ORYCTOLAGUS CUNICULUS Host: ID:469008, ESCHERICHIA COLI , BL21(DE3) Plasmid name: PJC20
Links	UniProt: P58772, Sequence view
ID 3 : MYOE
Image
Description	MYOSIN IE HEAVY CHAIN
Type	polymer
Fragment	RESIDUES 1-697
Mutation	YES
Formula weight	79207.945 Da
Number of molecules	3
Ec	3.6.4.1
Source	Method: Isolated from a genetically manipulated source Gene: SLIME MOLD, AX2, ID:44689, DICTYOSTELIUM DISCOIDEUM Host: ID:44689, DICTYOSTELIUM DISCOIDEUM Plasmid name: PDXA-3H
Links	UniProt: Q03479, Sequence view
ID 4 : ADENOSINE-5'-DIPHOSPHATE
Image
Description	ADENOSINE-5'-DIPHOSPHATE
Type	non-polymer
Formula weight	427.203 Da
Number of molecules	5
Source	Method: Obtained synthetically
ID 5 : CALCIUM ION
Image
Description	CALCIUM ION
Type	non-polymer
Formula weight	40.080 Da
Number of molecules	5
Source	Method: Obtained synthetically

Sample
Assembly
Aggregation state	FILAMENT
Details	CMOS IMAGE FRAMES SELECTED BY POWER SPECTRUM
Name	F-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 2)
Buffer
Name	5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
Experiment
Reconstruction method	HELICAL
Specimen type	VITREOUS ICE CRYO EM
Sample preparation
pH	7.2
Sample concentration	0.01 mg/ml
Sample support
Details	HOLEY CARBON
Vitrification
Details	VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,

Electron Microscopy
Imaging
Microscope	model: OTHER
Details	BEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	200 kV
Electron dose	1.7 e/A**2
Illumination mode	LOW DOSE FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 169644 X, nominal: 80000 X
Cs	nominal: 4.1 mm
Nominal defocus	max: 1500 nm, min: 750 nm
Specimen holder
Temperature	77 Kelvin
Detector
Type	TEMCAM-F816
Image scans
Number digital images	836

Processing
2D projection selection
Number of particles	9650
Software name	SPARX
3D reconstruction
Actual pixel size	1.84 A/pix
CTF correction method	EACH PARTICLE
Details	SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1988 (DEPOSITION ID: 10379).
Method	IHRSR
Nominal pixel size	1.84 A/pix
Resolution	7.8 A
3D fitting
Method	GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH
Refinement Protocol	EM
Refinement Space	REAL
3D fitting list
PDB entry ID	3MFP;1LKX PDB-3mfp PDB-1lkx
Refine
Ls d res high	7.80 A
ID	1
Refine hist
D res high	7.80
Total atoms	33500
Ligand atoms	140
Protein atoms	33360