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- EMDB-44154: The structure of human cardiac F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-44154
TitleThe structure of human cardiac F-actin
Map dataFinal map used for model building. Post process and sharpening done in phenix using density modification scheme.
Sample
  • Complex: Human cardiac F-actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsactin / cardiac / human / sarcomere / CONTRACTILE PROTEIN
Function / homology
Function and homology information


actin-myosin filament sliding / cardiac myofibril assembly / actin filament-based movement / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / microfilament motor activity / RHOB GTPase cycle / myosin binding ...actin-myosin filament sliding / cardiac myofibril assembly / actin filament-based movement / cardiac muscle tissue morphogenesis / actomyosin structure organization / Striated Muscle Contraction / I band / microfilament motor activity / RHOB GTPase cycle / myosin binding / heart contraction / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / sarcomere / actin filament organization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / blood microparticle / hydrolase activity / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / extracellular space / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
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
Actin, alpha cardiac muscle 1
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDoran MH / Sousa D / Rynkiewicz MJ / Lehman W / Cammarato A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R56HL124091-01 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)5R01HL036153-33 United States
CitationJournal: To Be Published
Title: Structure of human cardiac actin
Authors: Doran MH / Rynkiewicz MJ / Sousa D / Cammarato A / Lehman W
History
DepositionMar 20, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44154.png

Downloads & links

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Map

FileDownload / File: emd_44154.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map used for model building. Post process and sharpening done in phenix using density modification scheme.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.06 Å/pix.
x 95 pix.
= 100.51 Å		1.06 Å/pix.
x 101 pix.
= 106.858 Å		1.06 Å/pix.
x 175 pix.
= 185.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.4308176 - 2.2998092
Average (Standard dev.)0.000000000006664 (±0.20214956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin905392
Dimensions10117595
Spacing95101175
CellA: 100.509995 Å / B: 106.857994 Å / C: 185.15 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Post-processed map in RELION.

Fileemd_44154_additional_1.map
AnnotationPost-processed map in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refinement from RELION without post-processing.

Fileemd_44154_additional_2.map
AnnotationRefinement from RELION without post-processing.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_44154_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_44154_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human cardiac F-actin

EntireName: Human cardiac F-actin
Components
  • Complex: Human cardiac F-actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Human cardiac F-actin

SupramoleculeName: Human cardiac F-actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: ACTC was expressed in Sf21 insect cells, using recombinant baculoviruses, and purified via gelsolin affinity chromatography
Source (natural)Organism: Spodoptera frugiperda (fall armyworm) / Strain: Sf21
Molecular weightTheoretical: 420 KDa

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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: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.07791 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDDEETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVLSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWISKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Details: 2 mmolL-1 Tris (pH 8), 0.2 mmolL-1 CaCl2, 0.2 mmolL-1 ATP, 0.5 mmolL-1 b-mercaptoethanol, 0.002% NaN3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.93 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.48 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133289
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE

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