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- EMDB-44777: CRYO-EM STRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT -

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Basic information

Entry
Database: EMDB / ID: EMD-44777
TitleCRYO-EM STRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT
Map dataSTRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT
Sample
  • Organelle or cellular component: CARDIAC ALPHA ACTIN M305L MUTANT
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsCYTOSKELETON / STRUCTURAL PROTEIN / filament
Function / homology
Function and homology information


actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / I band / RHOB GTPase cycle / microfilament motor activity ...actin filament-based movement / actin-myosin filament sliding / cardiac myofibril assembly / Formation of the dystrophin-glycoprotein complex (DGC) / cardiac muscle tissue morphogenesis / Striated Muscle Contraction / actomyosin structure organization / I band / RHOB GTPase cycle / microfilament motor activity / heart contraction / myosin binding / mesenchyme migration / skeletal muscle thin filament assembly / RHOA GTPase cycle / cardiac muscle contraction / actin filament organization / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / actin cytoskeleton / cell body / response to ethanol / blood microparticle / hydrolase activity / response to xenobiotic stimulus / focal adhesion / positive regulation of gene expression / negative regulation of apoptotic process / glutamatergic synapse / extracellular space / extracellular exosome / ATP binding / membrane / cytoplasm / cytosol
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 speciesMammalia (mammals) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsHuang 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)R01GM143539 United States
CitationJournal: To Be Published
Title: CRYO-EM STRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT
Authors: Huang HL / Heissler SM / Chinthalapudi K
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44777.png

Downloads & links

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Map

FileDownload / File: emd_44777.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT
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: 0.2
Minimum - Maximum-0.6893563 - 1.1380613
Average (Standard dev.)0.0028426163 (±0.049666815)
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: Half Map A

Fileemd_44777_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_44777_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 : CARDIAC ALPHA ACTIN M305L MUTANT

EntireName: CARDIAC ALPHA ACTIN M305L MUTANT
Components
  • Organelle or cellular component: CARDIAC ALPHA ACTIN M305L MUTANT
    • Protein or peptide: Actin, alpha cardiac muscle 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: CARDIAC ALPHA ACTIN M305L MUTANT

SupramoleculeName: CARDIAC ALPHA ACTIN M305L MUTANT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mammalia (mammals)
Molecular weightTheoretical: 168.076 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: 4 / 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: 41.825531 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: DDEETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG ...String:
DDEETTALVC DNGSGLVKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GII TNW DDMEKIWHHT FYNELRVAPE EHPTLLTEAP LNPKANREKM TQIMFETFNV PAMYVAIQAV LSLYASGRTT GIVLDSG DG VTHNVPIYEG YALPHAIMRL DLAGRDLTDY LMKILTERGY SFVTTAEREI VRDIKEKLCY VALDFENEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PETLFQPSFI GMESAGIHET TYNSIMKCDI DIRKDLYANN VLSGGTTLYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDEAG PSIVHRKCF

UniProtKB: Actin, alpha cardiac muscle 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 4 / 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: 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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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 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5275 / 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: 2.5 µm / Nominal defocus min: 0.5 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 #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dmy

Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 383990
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dmy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 383990
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8dmy


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bph:
CRYO-EM STRUCTURE OF CARDIAC MUSCLE ALPHA-ACTIN M305L HCM MUTANT

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