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- PDB-9e2e: The structure of the junction region of the wild-type murine nati... -

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Basic information

Entry
Database: PDB / ID: 9e2e
TitleThe structure of the junction region of the wild-type murine native cardiac thin filament in Ca2+-free state
Components
  • Actin, alpha cardiac muscle 1
  • Isoform A2 of Troponin T, cardiac muscle
  • Tropomyosin alpha-1 chain
KeywordsMOTOR PROTEIN / thin filament / troponin T / muscle
Function / homology
Function and homology information


atrial cardiac muscle tissue morphogenesis / 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) / Striated Muscle Contraction / troponin C binding / RHOA GTPase cycle / Smooth Muscle Contraction ...atrial cardiac muscle tissue morphogenesis / 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) / Striated Muscle Contraction / troponin C binding / RHOA GTPase cycle / Smooth Muscle Contraction / cardiac Troponin complex / troponin complex / actin-myosin filament sliding / regulation of muscle contraction / cardiac myofibril assembly / negative regulation of ATP-dependent activity / cardiac muscle tissue morphogenesis / positive regulation of ATP-dependent activity / actomyosin structure organization / muscle filament sliding / I band / sarcomere organization / 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 / sarcoplasm / skeletal muscle thin filament assembly / cardiac muscle contraction / muscle contraction / sarcomere / filopodium / actin filament / response to bacterium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / response to calcium ion / actin filament binding / lamellipodium / actin cytoskeleton / actin binding / heart development / cell body / in utero embryonic development / response to ethanol / hydrolase activity / protein heterodimerization activity / response to xenobiotic stimulus / synapse / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / protein homodimerization activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Troponin T / Troponin / Troponin domain superfamily / Troponin / Tropomyosins signature. / Tropomyosin / Tropomyosin / 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 / Troponin T, 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: 4 Å
AuthorsGalkin, V.E. / Risi, C.M.
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: The structure of the junction region of the murine wild-type native cardiac thin filament.
Authors: Galkin, V.E. / Risi, C.M.
History
DepositionOct 22, 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

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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: Tropomyosin alpha-1 chain
H: Tropomyosin alpha-1 chain
I: Tropomyosin alpha-1 chain
J: Tropomyosin alpha-1 chain
K: Isoform A2 of Troponin T, cardiac muscle
L: Tropomyosin alpha-1 chain
M: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
O: Tropomyosin alpha-1 chain
P: Isoform A2 of Troponin T, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,21628
Polymers583,50716
Non-polymers2,70912
Water00
1


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

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Components

#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
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32735.609 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P58771
#3: Protein Isoform A2 of Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 34616.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P50752
#4: 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
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
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: junction region of cardiac thin filament / Type: COMPLEX / Entity ID: #1-#3 / 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: 33178

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2EPUimage acquisition
4RELIONCTF correction
7PHENIX1.2model fitting
9PHENIX1.2model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7170762
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68660 / Details: filtered map to 4.2 A / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17KO4

7ko4

17KO41PDBexperimental model
28DD0

8dd0

18DD02PDBexperimental model

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