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- EMDB-27572: Cryo-EM structure of nonmuscle beta-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-27572
TitleCryo-EM structure of nonmuscle beta-actin
Map dataCryo-EM structure of nonmuscle beta-actin
Sample
  • Organelle or cellular component: filamentous actin
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Regulation of CDH1 Function / bBAF complex / cellular response to cytochalasin B / npBAF complex ...positive regulation of norepinephrine uptake / Formation of the polybromo-BAF (pBAF) complex / Formation of the non-canonical BAF (ncBAF) complex / Formation of the canonical BAF (cBAF) complex / Formation of the embryonic stem cell BAF (esBAF) complex / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / Regulation of CDH1 Function / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Gap junction degradation / Folding of actin by CCT/TriC / GBAF complex / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / protein localization to adherens junction / dense body / Tat protein binding / postsynaptic actin cytoskeleton / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / apical junction complex / positive regulation of double-strand break repair / maintenance of blood-brain barrier / regulation of norepinephrine uptake / nitric-oxide synthase binding / transporter regulator activity / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / Recycling pathway of L1 / establishment or maintenance of cell polarity / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / kinesin binding / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / nitric-oxide synthase regulator activity / FCGR3A-mediated phagocytosis / adherens junction / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / Signaling by high-kinase activity BRAF mutants / RHO GTPases Activate Formins / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / kinetochore / structural constituent of cytoskeleton / B-WICH complex positively regulates rRNA expression / DNA Damage Recognition in GG-NER / VEGFA-VEGFR2 Pathway / platelet aggregation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / tau protein binding / Schaffer collateral - CA1 synapse / nuclear matrix / cytoplasmic ribonucleoprotein granule / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cell-cell junction / Signaling by BRAF and RAF1 fusions / UCH proteinases / nucleosome
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, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 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 11, 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_27572.png

Downloads & links

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Map

FileDownload / File: emd_27572.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of nonmuscle beta-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: 0.17
Minimum - Maximum-0.5888791 - 1.2353635
Average (Standard dev.)0.0086868815 (±0.043416437)
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 nonmuscle beta-actin

Fileemd_27572_half_map_1.map
AnnotationCryo-EM structure of nonmuscle beta-actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of nonmuscle beta-actin

Fileemd_27572_half_map_2.map
AnnotationCryo-EM structure of nonmuscle beta-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 : filamentous actin

EntireName: filamentous actin
Components
  • Organelle or cellular component: filamentous actin
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: filamentous actin

SupramoleculeName: filamentous actin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.69052 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: (ACE)DDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE (HIC)GIVTNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRT TGIVMDSGDG ...String:
(ACE)DDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE (HIC)GIVTNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRT TGIVMDSGDG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSLE KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP G IADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

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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 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
Detailsfilamentous beta actin with Mg. ADP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy 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: 1352 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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 selectionNumber selected: 263911
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6djo

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 263911
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6djo

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 81
Output model

PDB-8dnh:
Cryo-EM structure of nonmuscle beta-actin

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