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