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- PDB-4a7n: Structure of bare F-actin filaments obtained from the same sample... -

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Basic information

Entry
Database: PDB / ID: 4a7n
TitleStructure of bare F-actin filaments obtained from the same sample as the Actin-Tropomyosin-Myosin Complex
ComponentsF-ACTINActin
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / MYOSIN BINDING / ACTIN BINDING
Function / homology
Function and homology information


cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament ...cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsBehrmann, E. / Mueller, M. / Penczek, P.A. / Mannherz, H.G. / Manstein, D.J. / Raunser, S.
CitationJournal: Cell / 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 /
Abstract: Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions ...Regulation of myosin and filamentous actin interaction by tropomyosin is a central feature of contractile events in muscle and nonmuscle cells. However, little is known about molecular interactions within the complex and the trajectory of tropomyosin movement between its "open" and "closed" positions on the actin filament. Here, we report the 8 Å resolution structure of the rigor (nucleotide-free) actin-tropomyosin-myosin complex determined by cryo-electron microscopy. The pseudoatomic model of the complex, obtained from fitting crystal structures into the map, defines the large interface involving two adjacent actin monomers and one tropomyosin pseudorepeat per myosin contact. Severe forms of hereditary myopathies are linked to mutations that critically perturb this interface. Myosin binding results in a 23 Å shift of tropomyosin along actin. Complex domain motions occur in myosin, but not in actin. Based on our results, we propose a structural model for the tropomyosin-dependent modulation of myosin binding to actin.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id

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Assembly

Deposited unit
A: F-ACTIN
B: F-ACTIN
C: F-ACTIN
D: F-ACTIN
E: F-ACTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,71515
Polymers209,3785
Non-polymers2,33610
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
F-ACTIN / Actin


Mass: 41875.633 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: SKELETAL MUSCLE / References: UniProt: P68135
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BARE F-ACTIN FILAMENTS / Type: COMPLEX / Details: CMOS IMAGE FRAME SELECTED BY POWER SPECTRUM
Buffer solutionName: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININE
pH: 7.2
Details: 5MM TRIS, 100MM KCL, 2MM MGCL2, 50MM GLUTAMINE, 50MM ARGININE
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

MicroscopyModel: 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 FIELDBright-field microscopy / Nominal magnification: 80000 X / Calibrated magnification: 169644 X / Nominal defocus max: 1500 nm / Nominal defocus min: 750 nm / Cs: 4.1 mm
Specimen holderTemperature: 77 K
Image recordingElectron dose: 17 e/Å2 / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k)
Image scansNum. digital images: 836
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DireXmodel fitting
2SPARX3D reconstruction
CTF correctionDetails: EACH PARTICLE
3D reconstructionMethod: IHRSR / Resolution: 8.9 Å / Num. of particles: 4626 / Nominal pixel size: 1.84 Å / Actual pixel size: 1.84 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1990.(DEPOSITION ID: 10381).
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--GEOMETRY-BASED CONFORMATIONAL SAMPLING USING DEFORMABLE ELASTIC NETWORK (DEN) APPROACH REFINEMENT PROTOCOL--EM
Atomic model buildingPDB-ID: 3MFP

3mfp

RefinementHighest resolution: 8.9 Å
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14670 0 140 0 14810

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