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- EMDB-47712: The structure of the native cardiac thin filament in calcium free... -

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Basic information

Entry
Database: EMDB / ID: EMD-47712
TitleThe structure of the native cardiac thin filament in calcium free conditions in the presence of Lmod2
Map dataThe structure of the native cardiac thin filament in calcium free conditions in the presence of Lmod2
Sample
  • Complex: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
    • Complex: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
Keywordscardiac thin filament / Lmod2 / cryo-EM / MOTOR PROTEIN
Biological speciesSus scrofa (pig) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsRisi CM / Galkin VE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: PLoS Biol / Year: 2025
Title: Interaction of cardiac leiomodin with the native cardiac thin filament.
Authors: Madison Little / Cristina M Risi / Tania M Larrinaga / Mason D Summers / Tyler Nguyen / Garry E Smith / Jennifer Atherton / Carol C Gregorio / Alla S Kostyukova / Vitold E Galkin /
Abstract: Every heartbeat depends on cyclical contraction-relaxation produced by the interactions between myosin-containing thick and actin-based thin filaments (TFs) arranged into a crystalline-like lattice ...Every heartbeat depends on cyclical contraction-relaxation produced by the interactions between myosin-containing thick and actin-based thin filaments (TFs) arranged into a crystalline-like lattice in the cardiac sarcomere. Therefore, the maintenance of thin filament length is crucial for myocardium function. The thin filament is comprised of an actin backbone, the regulatory troponin complex and tropomyosin that controls interactions between thick and thin filaments. Thin filament length is controlled by the tropomodulin family of proteins; tropomodulin caps pointed ends of thin filaments, and leiomodin (Lmod) promotes elongation of thin filaments by a "leaky-cap" mechanism. The broader distribution of Lmod on the thin filament implied to the possibility of its interaction with the sides of thin filaments. Here, we use biochemical and structural approaches to show that cardiac Lmod (Lmod2) binds to a specific region on the native cardiac thin filament in a Ca2+-dependent manner. We demonstrate that Lmod2's unique C-terminal extension is required for binding to the thin filament actin backbone and suggest that interactions with the troponin complex assist Lmod2's localization on the surface of thin filaments. We propose that Lmod2 regulates the length of cardiac thin filaments in a working myocardium by protecting newly formed thin filament units during systole and promoting actin polymerization at thin filament pointed ends during diastole.
History
DepositionNov 5, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47712.png

Downloads & links

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Map

FileDownload / File: emd_47712.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe structure of the native cardiac thin filament in calcium free conditions in the presence of Lmod2
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: 0.0096
Minimum - Maximum-0.008442627 - 0.047270503
Average (Standard dev.)0.0001439235 (±0.0025331278)
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: Half Map A

Fileemd_47712_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47712_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Lmod2 with native cardiac thin filament in calcium fre...

EntireName: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
Components
  • Complex: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
    • Complex: Complex of Lmod2 with native cardiac thin filament in calcium free conditions

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Supramolecule #1: Complex of Lmod2 with native cardiac thin filament in calcium fre...

SupramoleculeName: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #2: Complex of Lmod2 with native cardiac thin filament in calcium fre...

SupramoleculeName: Complex of Lmod2 with native cardiac thin filament in calcium free conditions
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7314 / 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: 1767535
CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ko4

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Details: 6.2 Angstrom map filtered to 9A / Number images used: 25527
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

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