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- PDB-9mox: Structure of native murine cardiac thin filament variant I79N in ... -

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Basic information

Entry
Database: PDB / ID: 9mox
TitleStructure of native murine cardiac thin filament variant I79N in troponin T at pCa=5.8 in Ca2+-bound partially activated state (lower strand)
Components
  • Actin, alpha cardiac muscle 1
  • Isoform 6 of Troponin T, cardiac muscle
  • Tropomyosin alpha-1 chain
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
KeywordsMOTOR PROTEIN / thin filament / cryo-EM / troponin / tropomyosin / muscle structure
Function / homology
Function and homology information


actin-mediated cell contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction / RHOA GTPase cycle ...actin-mediated cell contraction / positive regulation of heart rate by epinephrine / muscle thin filament tropomyosin / RHOB GTPase cycle / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of systemic arterial blood pressure by ischemic conditions / Striated Muscle Contraction / troponin C binding / diaphragm contraction / RHOA GTPase cycle / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / Smooth Muscle Contraction / cardiac myofibril / cardiac Troponin complex / troponin complex / actin-myosin filament sliding / regulation of muscle contraction / cardiac myofibril assembly / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / Ion homeostasis / cardiac muscle tissue morphogenesis / positive regulation of ATP-dependent activity / actomyosin structure organization / Striated Muscle Contraction / muscle filament sliding / response to metal ion / I band / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / microfilament motor activity / myosin binding / regulation of heart contraction / tropomyosin binding / troponin I binding / myofibril / mesenchyme migration / striated muscle thin filament / skeletal muscle thin filament assembly / calcium channel inhibitor activity / vasculogenesis / striated muscle contraction / cardiac muscle contraction / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / response to calcium ion / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / heart development / cell body / in utero embryonic development / response to ethanol / hydrolase activity / protein domain specific binding / protein heterodimerization activity / response to xenobiotic stimulus / synapse / calcium ion binding / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / glutamatergic synapse / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / EF-hand domain pair / : / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Troponin C, slow skeletal and cardiac muscles / Troponin T, cardiac muscle / Troponin I, cardiac muscle / Tropomyosin alpha-1 chain / Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.2 Å
AuthorsRisi, C.M. / Galkin, V.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL160966 United States
CitationJournal: To Be Published
Title: Structure of native murine cardiac thin filament variant I79N in troponin T at pCa=5.8 in Ca2+-bound partially activated state (lower strand)
Authors: Risi, C.M. / Galkin, V.E.
History
DepositionDec 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha cardiac muscle 1
B: Actin, alpha cardiac muscle 1
C: Actin, alpha cardiac muscle 1
D: Actin, alpha cardiac muscle 1
E: Actin, alpha cardiac muscle 1
F: Actin, alpha cardiac muscle 1
G: Troponin C, slow skeletal and cardiac muscles
H: Troponin I, cardiac muscle
I: Isoform 6 of Troponin T, cardiac muscle
J: Isoform 6 of Troponin T, cardiac muscle
K: Tropomyosin alpha-1 chain
L: Tropomyosin alpha-1 chain
M: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)498,22829
Polymers495,39914
Non-polymers2,82915
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 14 molecules ABCDEFGHIJKLMN

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


Mass: 42064.891 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68033, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 18437.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P19123
#3: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 24308.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P48787
#4: Protein Isoform 6 of Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 34660.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P45379
#5: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32735.609 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771

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Non-polymers , 3 types, 15 molecules

#6: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
Has protein modificationN

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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: Native murine cardiac thin filament variant I79N in troponin T at pCa=5.8
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 17361

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4RELIONCTF correction
7PHENIXmodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7615631
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59174 / Algorithm: BACK PROJECTION / Details: filtered to 7 Angstroms / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17KO5

7ko5

17KO51PDBexperimental model
27UTI

7uti

17UTI2PDBexperimental model
38V0K

8v0k

18V0K3PDBexperimental model
41AF-P50752-F1-v44AlphaFoldin silico model

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