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- EMDB-42800: The structure of the native cardiac thin filament troponin core i... -

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Basic information

Entry
Database: EMDB / ID: EMD-42800
TitleThe structure of the native cardiac thin filament troponin core in Ca2+-free state from the lower strand
Map data
Sample
  • Complex: thin filament troponin core complex
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
    • Protein or peptide: Troponin I, cardiac muscle
    • Protein or peptide: Troponin T2, cardiac type
    • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsthin filament / troponin / tropomyosin / cryo-EM / muscle structure / MOTOR PROTEIN
Function / homology
Function and homology information


Striated Muscle Contraction / cardiac Troponin complex / actin-myosin filament sliding / troponin complex / regulation of muscle contraction / myosin binding / heart contraction / mesenchyme migration / troponin I binding / skeletal muscle contraction ...Striated Muscle Contraction / cardiac Troponin complex / actin-myosin filament sliding / troponin complex / regulation of muscle contraction / myosin binding / heart contraction / mesenchyme migration / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / sarcomere / filopodium / actin filament organization / actin filament / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / cell body / protein heterodimerization activity / calcium ion binding / positive regulation of gene expression / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Tropomyosins signature. / Troponin / Troponin domain superfamily / Troponin / Tropomyosin / Tropomyosin ...Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Tropomyosins signature. / Troponin / Troponin domain superfamily / Troponin / 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
Troponin I, cardiac muscle / Troponin T, cardiac muscle / Actin, alpha cardiac muscle 1 / Tropomyosin alpha-1 chain / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsGalkin VE / Risi CM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL160966 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL140925 United States
CitationJournal: J Mol Biol / Year: 2024
Title: Troponin Structural Dynamics in the Native Cardiac Thin Filament Revealed by Cryo Electron Microscopy.
Authors: Cristina M Risi / Betty Belknap / Jennifer Atherton / Isabella Leite Coscarella / Howard D White / P Bryant Chase / Jose R Pinto / Vitold E Galkin /
Abstract: Cardiac muscle contraction occurs due to repetitive interactions between myosin thick and actin thin filaments (TF) regulated by Ca levels, active cross-bridges, and cardiac myosin-binding protein C ...Cardiac muscle contraction occurs due to repetitive interactions between myosin thick and actin thin filaments (TF) regulated by Ca levels, active cross-bridges, and cardiac myosin-binding protein C (cMyBP-C). The cardiac TF (cTF) has two nonequivalent strands, each comprised of actin, tropomyosin (Tm), and troponin (Tn). Tn shifts Tm away from myosin-binding sites on actin at elevated Ca levels to allow formation of force-producing actomyosin cross-bridges. The Tn complex is comprised of three distinct polypeptides - Ca-binding TnC, inhibitory TnI, and Tm-binding TnT. The molecular mechanism of their collective action is unresolved due to lack of comprehensive structural information on Tn region of cTF. C1 domain of cMyBP-C activates cTF in the absence of Ca to the same extent as rigor myosin. Here we used cryo-EM of native cTFs to show that cTF Tn core adopts multiple structural conformations at high and low Ca levels and that the two strands are structurally distinct. At high Ca levels, cTF is not entirely activated by Ca but exists in either partially or fully activated state. Complete dissociation of TnI C-terminus is required for full activation. In presence of cMyBP-C C1 domain, Tn core adopts a fully activated conformation, even in absence of Ca. Our data provide a structural description for the requirement of myosin to fully activate cTFs and explain increased affinity of TnC to Ca in presence of active cross-bridges. We suggest that allosteric coupling between Tn subunits and Tm is required to control actomyosin interactions.
History
DepositionNov 13, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42800.png

Downloads & links

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Map

FileDownload / File: emd_42800.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 324 pix.
= 439.344 Å		1.36 Å/pix.
x 324 pix.
= 439.344 Å		1.36 Å/pix.
x 324 pix.
= 439.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.88
Minimum - Maximum-3.9733353 - 9.618808
Average (Standard dev.)0.00014675058 (±0.1280983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 439.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42800_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42800_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : thin filament troponin core complex

EntireName: thin filament troponin core complex
Components
  • Complex: thin filament troponin core complex
    • Protein or peptide: Actin, alpha cardiac muscle 1
    • Protein or peptide: Troponin C, slow skeletal and cardiac muscles
    • Protein or peptide: Troponin I, cardiac muscle
    • Protein or peptide: Troponin T2, cardiac type
    • Protein or peptide: Tropomyosin alpha-1 chain
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: thin filament troponin core complex

SupramoleculeName: thin filament troponin core complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Actin, alpha cardiac muscle 1

MacromoleculeName: Actin, alpha cardiac muscle 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 42.064891 KDa
SequenceString: MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVLSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: Troponin C, slow skeletal and cardiac muscles

MacromoleculeName: Troponin C, slow skeletal and cardiac muscles / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 18.433508 KDa
SequenceString:
MDDIYKAAVE QLTEEQKNEF KAAFDIFVLG AEDGCISTKE LGKVMRMLGQ NPTPEELQEM IDEVDEDGSG TVDFDEFLVM MVRCMKDDS KGKSEEELSD LFRMFDKNAD GYIDLEELKI MLQATGETIT EDDIEELMKD GDKNNDGRID YDEFLEFMKG V E

UniProtKB: Troponin C, slow skeletal and cardiac muscles

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Macromolecule #3: Troponin I, cardiac muscle

MacromoleculeName: Troponin I, cardiac muscle / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 24.09268 KDa
SequenceString: MADRSGDAAG DSRPAPAPVR RRSSANYRAY ATEPHAKKKS KISASRKLQL KTLMLQIAKQ ELEREAEERR GEKGRALSTR CQPLELAGL SFAELQDLCR QLHARVDKVD EERYDVEAKV TKNITEIADL NQKIFDLRGK FKRPTLRRVR ISADAMMQAL L GARAKETL ...String:
MADRSGDAAG DSRPAPAPVR RRSSANYRAY ATEPHAKKKS KISASRKLQL KTLMLQIAKQ ELEREAEERR GEKGRALSTR CQPLELAGL SFAELQDLCR QLHARVDKVD EERYDVEAKV TKNITEIADL NQKIFDLRGK FKRPTLRRVR ISADAMMQAL L GARAKETL DLRAHLKQVK KEDTEKENRE VGDWRKNIDA LSGMEGRKKK FEG

UniProtKB: Troponin I, cardiac muscle

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Macromolecule #4: Troponin T2, cardiac type

MacromoleculeName: Troponin T2, cardiac type / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 33.941738 KDa
SequenceString: MSDVEETVDE YEEEQEEGAA EEQEEAVEEE AGGEAEAEEA NAEEAGQEED GREAEDGPME ESKPKPRLFM PNLVPPKIPD GERVDFDDI HRKRMKDLNE LQTLIEAHFE NRKKEEELVS LKDRIEKRRA ERAEQQRIRT EREKERQTRL AEERARREEE E NRRKAEDE ...String:
MSDVEETVDE YEEEQEEGAA EEQEEAVEEE AGGEAEAEEA NAEEAGQEED GREAEDGPME ESKPKPRLFM PNLVPPKIPD GERVDFDDI HRKRMKDLNE LQTLIEAHFE NRKKEEELVS LKDRIEKRRA ERAEQQRIRT EREKERQTRL AEERARREEE E NRRKAEDE ARKKKALSNM MHFGGYIQKQ AQTERKSGKR QTEREKKKKI LAERRKVLAI DHLNEDQLRE KAKELWQSIY NL EAEKFDL QEKFKQQKYE INVLRNRIND NQKVSKTRGK AKVTGRWK

UniProtKB: Troponin T, cardiac muscle

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Macromolecule #5: Tropomyosin alpha-1 chain

MacromoleculeName: Tropomyosin alpha-1 chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 32.762656 KDa
SequenceString: MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKRLE DELVSLQKKL KATEDELDKY SEAPKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK ...String:
MDAIKKKMQM LKLDKENALD RAEQAEADKK AAEDRSKRLE DELVSLQKKL KATEDELDKY SEAPKDAQEK LELAEKKATD AEADVASLN RRIQLVEEEL DRAQERLATA LQKLEEAEKA ADESERGMKV IESRAQKDEE KMEIQEIQLK EAKHIAEDAD R KYEEVARK LVIIESDLER AEERAELSEG KCAELEEELK TVTNNLKSLE AQAEKYSQKE DKYEEEIKVL SDKLKEAETR AE FAERSVT KLEKSIDDLE DELYAQKLKY KAISEELDHA LNDMTSI

UniProtKB: Tropomyosin alpha-1 chain

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 24133 / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7379204
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ko4


Details: Model filtered to 30A resolution
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Details: Filtered to 8A / Number images used: 91835
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.08)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.08)
Final 3D classificationSoftware - Name: RELION (ver. 3.08) / Details: Unsupervised 3D sorting
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7ko4

source_name: PDB, initial_model_type: experimental model

7utl

source_name: PDB, initial_model_type: experimental model

8ddo
PDB Unreleased entry

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8uyd:
The structure of the native cardiac thin filament troponin core in Ca2+-free state from the lower strand

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