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- EMDB-27549: Cryo-EM structure of cardiac muscle alpha-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-27549
TitleCryo-EM structure of cardiac muscle alpha-actin
Map dataCryo-EM structure of cardiac muscle alpha-actin
Sample
  • Organelle or cellular component: cardiac alpha actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / heart contraction / myosin binding / mesenchyme migration / actin filament organization / sarcomere / actin filament / filopodium ...Striated Muscle Contraction / RHOA GTPase cycle / actin-myosin filament sliding / heart contraction / myosin binding / mesenchyme migration / actin filament organization / sarcomere / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / hydrolase activity / positive regulation of gene expression / ATP binding / 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 speciesBos taurus (domestic cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsArora AS / Huang HL / Heissler SM / Chinthalapudi K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143539 United States
CitationJournal: Elife / Year: 2023
Title: Structural insights into actin isoforms.
Authors: Amandeep S Arora / Hsiang-Ling Huang / Ramanpreet Singh / Yoshie Narui / Andrejus Suchenko / Tomoyuki Hatano / Sarah M Heissler / Mohan K Balasubramanian / Krishna Chinthalapudi /
Abstract: Actin isoforms organize into distinct networks that are essential for the normal function of eukaryotic cells. Despite a high level of sequence and structure conservation, subtle differences in their ...Actin isoforms organize into distinct networks that are essential for the normal function of eukaryotic cells. Despite a high level of sequence and structure conservation, subtle differences in their design principles determine the interaction with myosin motors and actin-binding proteins. Therefore, identifying how the structure of actin isoforms relates to function is important for our understanding of normal cytoskeletal physiology. Here, we report the high-resolution structures of filamentous skeletal muscle α-actin (3.37 Å), cardiac muscle α-actin (3.07 Å), ß-actin (2.99 Å), and γ-actin (3.38 Å) in the Mg·ADP state with their native post-translational modifications. The structures revealed isoform-specific conformations of the N-terminus that shift closer to the filament surface upon myosin binding, thereby establishing isoform-specific interfaces. Collectively, the structures of single-isotype, post-translationally modified bare skeletal muscle α-actin, cardiac muscle α-actin, ß-actin, and γ-actin reveal general principles, similarities, and differences between isoforms. They complement the repertoire of known actin structures and allow for a comprehensive understanding of in vitro and in vivo functions of actin isoforms.
History
DepositionJul 9, 2022-
Header (metadata) releaseApr 12, 2023-
Map releaseApr 12, 2023-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27549.png

Downloads & links

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Map

FileDownload / File: emd_27549.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of cardiac muscle alpha-actin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 256 pix.
= 228.096 Å		0.89 Å/pix.
x 256 pix.
= 228.096 Å		0.89 Å/pix.
x 256 pix.
= 228.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.205
Minimum - Maximum-0.9155103 - 1.4391645
Average (Standard dev.)0.0019578366 (±0.049385447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 228.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of cardiac muscle alpha-actin

Fileemd_27549_half_map_1.map
AnnotationCryo-EM structure of cardiac muscle alpha-actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of cardiac muscle alpha-actin

Fileemd_27549_half_map_2.map
AnnotationCryo-EM structure of cardiac muscle alpha-actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : cardiac alpha actin

EntireName: cardiac alpha actin
Components
  • Organelle or cellular component: cardiac alpha actin
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: cardiac alpha actin

SupramoleculeName: cardiac alpha actin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Cardiac actin extracted and purified from bovine heart
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Heart / Tissue: Left Ventricle

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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: 4 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: cattle (cattle) / Organ: Heart / Tissue: left ventricle muscle
Molecular weightTheoretical: 41.72848 KDa
SequenceString: DEETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIIT NWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGD GV THNVPIYEGY ...String:
DEETTALVCD NGSGLVKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIIT NWD DMEKIWHHTF YNELRVAPEE HPTLLTEAPL NPKANREKMT QIMFETFNVP AMYVAIQAVL SLYASGRTTG IVLDSGD GV THNVPIYEGY ALPHAIMRLD LAGRDLTDYL MKILTERGYS FVTTAEREIV RDIKEKLCYV ALDFENEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP ETLFQPSFIG MESAGIHETT YNSIMKCDID IRKDLYANNV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDEAGP SIVHRKCF

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / 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: C-flat / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs-corrected microscope / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1444 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 81000
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 selectionDetails: Single Particle
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6djo

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 657041
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6djo


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 117
Output model

PDB-8dmy:
Cryo-EM structure of cardiac muscle alpha-actin

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