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

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Database: PDB / ID: 5noj
TitleCa2+-induced Movement of Tropomyosin on Native Cardiac Thin Filaments - "OPEN" state
  • Actin, alpha skeletal muscle
  • cardiac alpha tropomyosin
KeywordsMOTOR PROTEIN / F-actin / tropomyosin / motor protein
Specimen sourceSus scrofa / mammal / Pig (Wikipedia) / image: Sus scrofa domestica
MethodElectron microscopy (11 Å resolution / Helical array / Helical)
AuthorsRisi, C. / Eisner, J. / Belknap, B. / Heeley, D.H. / White, H.D. / Schroeder, G.F. / Galkin, V.E.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 6782-6787

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 6782-6787 Yorodumi Papers
Ca-induced movement of tropomyosin on native cardiac thin filaments revealed by cryoelectron microscopy.
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: Aug 2, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelDatabase referencescitation / citation_author_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name

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Deposited unit
A: Actin, alpha skeletal muscle
B: Actin, alpha skeletal muscle
C: Actin, alpha skeletal muscle
D: Actin, alpha skeletal muscle
E: Actin, alpha skeletal muscle
F: cardiac alpha tropomyosin
H: cardiac alpha tropomyosin
hetero molecules

Theoretical massNumber of molelcules
Total (without water)229,53417

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)19430
ΔGint (kcal/M)-208
Surface area (Å2)84260


#1: Protein/peptide
Actin, alpha skeletal muscle / Alpha-actin-1

Mass: 40818.477 Da / Num. of mol.: 5
Source: (gene. exp.) Sus scrofa / mammal / Pig (Wikipedia) / image: Sus scrofa domestica
Gene: ACTA1, ACTA / Production host: Sus scrofa / References: UniProt: P68137
#2: Protein/peptide cardiac alpha tropomyosin

Mass: 11592.281 Da / Num. of mol.: 2
Source: (gene. exp.) Sus scrofa / mammal / Pig (Wikipedia) / image: Sus scrofa domestica
Production host: Sus scrofa
#3: Chemical

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

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

Experimental details


EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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
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 %

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 FIELD
Image recordingElectron dose: 3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)


EM software
Helical symmertyAngular rotation/subunit: -166.7 deg. / Axial rise/subunit: 27.4 Å / Axial symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 3809 / 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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