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- PDB-5nol: Ca2+-induced Movement of Tropomyosin on Native Cardiac Thin Filam... -

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Basic information

Entry
Database: PDB / ID: 5nol
TitleCa2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "Closed" state
Components
  • Cardiac muscle alpha actin 1
  • cardiac alpha tropomyosin
KeywordsMOTOR PROTEIN / F-actin / tropomyosin / motor protein
Function / homologyActin/actin-like conserved site / Striated Muscle Contraction / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / Actin family / Actin, conserved site / actomyosin, actin portion / actin-myosin filament sliding ...Actin/actin-like conserved site / Striated Muscle Contraction / Actins and actin-related proteins signature. / Actins signature 2. / Actins signature 1. / Actin / Actin family / Actin, conserved site / actomyosin, actin portion / actin-myosin filament sliding / cardiac myofibril assembly / mesenchyme migration / cardiac muscle tissue morphogenesis / I band / myosin binding / heart contraction / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / filopodium / actin filament / cell body / lamellipodium / ATPase activity / glutamatergic synapse / positive regulation of gene expression / negative regulation of apoptotic process / ATP binding / cytoplasm / Cardiac muscle alpha actin 1 / Actin, alpha skeletal muscle
Function and homology information
Specimen sourceSus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 8 Å resolution
AuthorsRisi, C. / Eisner, J. / Belknap, B. / Heeley, D.H. / White, H.D. / Schroeder, G.F. / Galkin, V.E.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Ca-induced movement of tropomyosin on native cardiac thin filaments revealed by cryoelectron microscopy.
Authors: Cristina Risi / Jamie Eisner / Betty Belknap / David H Heeley / Howard D White / Gunnar F Schröder / Vitold E Galkin
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2017 / Release: Jul 19, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 19, 2017Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_image_scans_em_3d_fitting.target_criteria
1.2Nov 21, 2018Structure modelAdvisory / Data collection / Derived calculationsem_software / pdbx_validate_close_contact / struct_conn / struct_conn_type_em_software.name

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Cardiac muscle alpha actin 1
B: Cardiac muscle alpha actin 1
C: Cardiac muscle alpha actin 1
D: Cardiac muscle alpha actin 1
E: Cardiac muscle alpha actin 1
F: cardiac alpha tropomyosin
G: cardiac alpha tropomyosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,29917
Polyers227,0427
Non-polymers2,25810
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)19490
ΔGint (kcal/M)-202
Surface area (Å2)84920
MethodPISA

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Components

#1: Protein/peptide
Cardiac muscle alpha actin 1


Mass: 40805.457 Da / Num. of mol.: 5 / Source: (gene. exp.) Sus scrofa (pig) / Gene: ACTC1 / Production host: Sus scrofa (pig) / References: UniProt: B6VNT8, UniProt: P68137*PLUS
#2: Protein/peptide cardiac alpha tropomyosin


Mass: 11507.176 Da / Num. of mol.: 2 / Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Native Cardiac Thin Filaments / Type: ORGANELLE OR CELLULAR COMPONENT / Details: Sample contains actin, tropomyosin, and troponin. / Entity ID: 1, 2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1EMAN2particle selection
4CTFFIND3CTF correction
7DireXmodel fitting
13SPIDER3D reconstructionIHRSR
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.8 deg. / Axial rise/subunit: 27.4 Å / Axial symmetry: C1
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 12356 / Symmetry type: HELICAL
Atomic model buildingDetails: Rigid fitting was done with Chimera and then DireX was used for flexible fitting.
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient

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