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- EMDB-49344: In situ structure of the cardiac thin filament without troponin f... -

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Basic information

Entry
Database: EMDB / ID: EMD-49344
TitleIn situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
Map dataIn situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7WT/WT)
Sample
  • Cell: In situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
Keywordscardiac thin filament / CONTRACTILE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 8.7 Å
AuthorsWoldeyes RA / Chiu W
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)2T32EB009035 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K99HL161392 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM139166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
CitationJournal: To Be Published
Title: Structure of the Thin Filament in Human iPSC-derived Cardiomyocytes and its Response to Heart Disease
Authors: Woldeyes RA / Chiu W
History
DepositionFeb 21, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49344.png

Downloads & links

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Map

FileDownload / File: emd_49344.map.gz / Format: CCP4 / Size: 122.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7WT/WT)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 318 pix.
= 677.34 Å		2.13 Å/pix.
x 318 pix.
= 677.34 Å		2.13 Å/pix.
x 318 pix.
= 677.34 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00164
Minimum - Maximum-0.0042868205 - 0.006912482
Average (Standard dev.)-0.0000041426306 (±0.0002569665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions318318318
Spacing318318318
CellA=B=C: 677.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49344_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_49344_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49344_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 : In situ structure of the cardiac thin filament without troponin f...

EntireName: In situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
Components
  • Cell: In situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))

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Supramolecule #1: In situ structure of the cardiac thin filament without troponin f...

SupramoleculeName: In situ structure of the cardiac thin filament without troponin from isogenic control human induced pluripotent stem cell-derived cardiomyocytes (AICS-0097-113 ACTN2-mEGFP MYH7(WT/WT))
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 16451
ExtractionNumber tomograms: 12 / Number images used: 92224
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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