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- PDB-4a7h: Structure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2) -

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Basic information

Entry
Database: PDB / ID: 4a7h
TitleStructure of the Actin-Tropomyosin-Myosin Complex (rigor ATM 2)
DescriptorACTIN
ALPHA SKELETAL MUSCLE
TROPOMYOSIN 1-ALPHA CHAIN
MYOSIN IE HEAVY CHAIN
KeywordsSTRUCTURAL PROTEIN/HYDROLASE / STRUCTURAL PROTEIN-HYDROLASE COMPLEX / STRUCTURAL PROTEIN / CYTOSKELETON / CONTRACTILE FILAMENT / MOTOR ACTIVITY / MYOSIN BINDING / ACTIN BINDING / ATP CATABOLIC PROCESS / RIGOR STATE
Specimen sourceOryctolagus cuniculus / mammal / RABBIT / アナウサギ /
Dictyostelium discoideum / fungus / SLIME MOLD /
MethodElectron microscopy (7.8 Å resolution / Filament / Helical)
AuthorsBehrmann, E. / Mueller, M. / Penczek, P.A. / Mannherz, H.G. / Manstein, D.J. / 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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2011 / Release: Aug 1, 2012
RevisionDateData content typeGroupProviderType
1.0Aug 1, 2012Structure modelrepositoryInitial release
1.1Apr 19, 2017Structure modelOther

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Assembly

Deposited unit
A: ACTIN, ALPHA SKELETAL MUSCLE
B: TROPOMYOSIN 1-ALPHA CHAIN
C: MYOSIN IE HEAVY CHAIN
D: ACTIN, ALPHA SKELETAL MUSCLE
E: ACTIN, ALPHA SKELETAL MUSCLE
F: ACTIN, ALPHA SKELETAL MUSCLE
G: ACTIN, ALPHA SKELETAL MUSCLE
H: TROPOMYOSIN 1-ALPHA CHAIN
I: MYOSIN IE HEAVY CHAIN
J: MYOSIN IE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,95220
Polyers478,61510
Non-polymers2,33610
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)
ACTIN, ALPHA SKELETAL MUSCLE / F-ACTIN / ALPHA-ACTIN-1


Mass: 41875.633 Da / Num. of mol.: 5
Source: (natural) Oryctolagus cuniculus / mammal / アナウサギ /
References: UniProt: P68135

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)TROPOMYOSIN 1-ALPHA CHAIN


Mass: 15807.628 Da / Num. of mol.: 2 / Fragment: RESIDUES 98-233
Source: (gene. exp.) Oryctolagus cuniculus / mammal / アナウサギ /
References: UniProt: P58772

Cellular component

Molecular function

#3: Polypeptide(L)MYOSIN IE HEAVY CHAIN / MYOE


Mass: 79207.305 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-697 / Mutation: YES / Source: (gene. exp.) Dictyostelium discoideum / fungus / / References: UniProt: Q03479, EC: 3.6.4.1

Cellular component

Molecular function

Biological process

#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP *YM


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Formula: Ca
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).

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

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Sample preparation

ComponentName: F-ACTIN-MYO1E-TROPOMYOSIN COMPLEX (CONFORMATION 2) / Type: COMPLEX / Details: CMOS IMAGE FRAMES SELECTED BY POWER SPECTRUM
Buffer solutionName: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
Details: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININ
pH: 7.2
SpecimenConc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, TEMPERATURE- 101, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- MANUAL BLOTTING FOR APPROXIMATELY 15 SECONDS,

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC
Details: BEST 836 MICROGRAPHS WERE SELECTED FROM OVER 3000 AQUIRED IMAGES
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 80000 / Calibrated magnification: 169644 / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 4.1 mm
Specimen holderTemperature: 77 kelvins
Image recordingElectron dose: 1.7 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Image scansNumber digital images: 836
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DireXMODEL FITTING
2SPARXRECONSTRUCTION
CTF correctionDetails: EACH PARTICLE
3D reconstructionMethod: IHRSR / Resolution: 7.8 Å / Number of particles: 9650 / Nominal pixel size: 1.84 / Actual pixel size: 1.84
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1988 (DEPOSITION ID: 10379).
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH REFINEMENT PROTOCOL--EM
Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
13MFP1
21LKX1
Least-squares processHighest resolution: 7.8 Å
Refine hist #LASTHighest resolution: 7.8 Å
Number of atoms included #LASTProtein: 33360 / Nucleic acid: 0 / Ligand: 140 / Solvent: 0 / Total: 33500

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