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- PDB-8dd0: The structure of the native cardiac thin filament junction region -

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Basic information

Entry
Database: PDB / ID: 8dd0
TitleThe structure of the native cardiac thin filament junction region
Components
  • Actin, alpha cardiac muscle 1
  • Tropomyosin alpha-1 chain
  • Troponin T2, cardiac type
KeywordsMOTOR PROTEIN / thin filament / actin / tropomyosin / troponin
Function / homology
Function and homology information


Striated Muscle Contraction / troponin C binding / cardiac myofibril / cardiac Troponin complex / actin-myosin filament sliding / troponin complex / regulation of muscle contraction / muscle filament sliding / ventricular cardiac muscle tissue morphogenesis / sarcomere organization ...Striated Muscle Contraction / troponin C binding / cardiac myofibril / cardiac Troponin complex / actin-myosin filament sliding / troponin complex / regulation of muscle contraction / muscle filament sliding / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / regulation of heart contraction / myosin binding / tropomyosin binding / heart contraction / mesenchyme migration / troponin I binding / cardiac muscle contraction / sarcomere / filopodium / actin filament organization / actin filament / response to calcium ion / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / protein heterodimerization activity / positive regulation of gene expression / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Tropomyosins signature. / Troponin / Troponin domain superfamily / Troponin / Tropomyosin / Tropomyosin / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Troponin T / Tropomyosins signature. / Troponin / Troponin domain superfamily / Troponin / 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 / Actin, alpha cardiac muscle 1 / Troponin T, cardiac muscle / Tropomyosin alpha-1 chain
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsGalkin, V.E. / Risi, C.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL160966 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116790 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL140925 United States
CitationJournal: PNAS Nexus / Year: 2023
Title: High-resolution cryo-EM structure of the junction region of the native cardiac thin filament in relaxed state.
Authors: Cristina M Risi / Betty Belknap / Howard D White / Kelly Dryden / Jose R Pinto / P Bryant Chase / Vitold E Galkin /
Abstract: Cardiac contraction depends on molecular interactions among sarcomeric proteins coordinated by the rising and falling intracellular Ca levels. Cardiac thin filament (cTF) consists of two strands ...Cardiac contraction depends on molecular interactions among sarcomeric proteins coordinated by the rising and falling intracellular Ca levels. Cardiac thin filament (cTF) consists of two strands composed of actin, tropomyosin (Tm), and equally spaced troponin (Tn) complexes forming regulatory units. Tn binds Ca to move Tm strand away from myosin-binding sites on actin to enable actomyosin cross-bridges required for force generation. The Tn complex has three subunits-Ca-binding TnC, inhibitory TnI, and Tm-binding TnT. Tm strand is comprised of adjacent Tm molecules that overlap "head-to-tail" along the actin filament. The N-terminus of TnT (e.g., TnT1) binds to the Tm overlap region to form the cTF junction region-the region that connects adjacent regulatory units and confers to cTF internal cooperativity. Numerous studies have predicted interactions among actin, Tm, and TnT1 within the junction region, although a direct structural description of the cTF junction region awaited completion. Here, we report a 3.8 Å resolution cryo-EM structure of the native cTF junction region at (pCa 8) Ca conditions. We provide novel insights into the "head-to-tail" interactions between adjacent Tm molecules and interactions between the Tm junction with F-actin. We demonstrate how TnT1 stabilizes the Tm overlap region via its interactions with the Tm C- and N-termini and actin. Our data show that TnT1 works as a joint that anchors the Tm overlap region to actin, which stabilizes the state of the cTF. Our structure provides insight into the molecular basis of cardiac diseases caused by missense mutations in TnT1.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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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: Tropomyosin alpha-1 chain
H: Tropomyosin alpha-1 chain
I: Tropomyosin alpha-1 chain
J: Tropomyosin alpha-1 chain
K: Troponin T2, cardiac type
L: Tropomyosin alpha-1 chain
M: Tropomyosin alpha-1 chain
N: Tropomyosin alpha-1 chain
O: Tropomyosin alpha-1 chain
P: Troponin T2, cardiac type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)587,51728
Polymers584,80816
Non-polymers2,70912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Actin, alpha cardiac muscle 1 / Cardiac muscle alpha actin 1


Mass: 42064.891 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / References: UniProt: B6VNT8
#2: Protein
Tropomyosin alpha-1 chain / Alpha-tropomyosin / Tropomyosin-1


Mass: 32762.656 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / References: UniProt: P42639
#3: Protein Troponin T2, cardiac type


Mass: 35158.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / References: UniProt: I3LS66
#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

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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 the native cardiac thin filament / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Sus scrofa (pig) / Organ: heart
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN 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 grids imaged: 5 / Num. of real images: 24133

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.08CTF correction
7PHENIXmodel fitting
9PHENIXmodel refinement
10RELION3.08initial Euler assignment
11RELION3.08final Euler assignment
12RELION3.08classification
13RELION3.083D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7379204
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236359 / Algorithm: BACK PROJECTION / Details: Filtered to 3.8 A resolution / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7KO4

7ko4


Accession code: 7KO4 / Source name: PDB / Type: experimental model

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