+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5170 | |||||||||
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Title | Binding of alpha-actinin CH1 to F-actin | |||||||||
Map data | reconstructed volume of F-actin decorated with alpha-actinin ABD (CH1 and CH2) | |||||||||
Sample |
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Keywords | helical filaments / calponin homology domains | |||||||||
Function / homology | Function and homology information positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of norepinephrine uptake / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / cellular response to cytochalasin B ...positive regulation of glucose catabolic process to lactate via pyruvate / negative regulation of relaxation of muscle / regulation of the force of skeletal muscle contraction / skeletal muscle atrophy / positive regulation of skeletal muscle fiber development / positive regulation of norepinephrine uptake / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / positive regulation of fast-twitch skeletal muscle fiber contraction / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / Formation of annular gap junctions / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / positive regulation of bone mineralization involved in bone maturation / Tat protein binding / muscle cell development / Folding of actin by CCT/TriC / regulation of double-strand break repair / transition between fast and slow fiber / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / negative regulation of oxidative phosphorylation / focal adhesion assembly / RHOF GTPase cycle / Striated Muscle Contraction / Adherens junctions interactions / bone morphogenesis / tight junction / Sensory processing of sound by outer hair cells of the cochlea / negative regulation of glycolytic process / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / negative regulation of cold-induced thermogenesis / Nephrin family interactions / regulation of norepinephrine uptake / positive regulation of double-strand break repair / structural constituent of muscle / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / negative regulation of calcineurin-NFAT signaling cascade / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / regulation of aerobic respiration / cortical actin cytoskeleton / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Recycling pathway of L1 / regulation of cyclin-dependent protein serine/threonine kinase activity / pseudopodium / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / cell projection / actin filament / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of transmembrane transporter activity / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / tau protein binding / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 15.0 Å | |||||||||
Authors | Galkin VE / Orlova A / Salmazo A / Djinovic-Carugo K / Egelman EH | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2010 Title: Opening of tandem calponin homology domains regulates their affinity for F-actin. Authors: Vitold E Galkin / Albina Orlova / Anita Salmazo / Kristina Djinovic-Carugo / Edward H Egelman / Abstract: Many actin-binding proteins contain calponin homology (CH) domains, but the manner in which these domains interact with F-actin has been controversial. Crystal structures have shown the tandem CH ...Many actin-binding proteins contain calponin homology (CH) domains, but the manner in which these domains interact with F-actin has been controversial. Crystal structures have shown the tandem CH domains of alpha-actinin to be in a compact, closed conformation, but the interpretations of complexes of such tandem CH domains with F-actin have been ambiguous. We show that the tandem CH domains of alpha-actinin bind F-actin in an open conformation, explaining mutations that cause human diseases and suggesting that the opening of these domains may be one of the main regulatory mechanisms for proteins with tandem CH domains. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5170.map.gz | 3.5 MB | EMDB map data format | |
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Header (meta data) | emd-5170-v30.xml emd-5170.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_5170_1.jpg | 62.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5170 | HTTPS FTP |
-Related structure data
Related structure data | 3lueMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5170.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | reconstructed volume of F-actin decorated with alpha-actinin ABD (CH1 and CH2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.38 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
Entire | Name: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2) |
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Components |
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-Supramolecule #1000: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2)
Supramolecule | Name: F-actin decorated with alpha-actinin ABD (containing CH1 and CH2) type: sample / ID: 1000 / Details: none / Oligomeric state: one to one binding / Number unique components: 2 |
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-Macromolecule #1: F-actin
Macromolecule | Name: F-actin / type: protein_or_peptide / ID: 1 / Name.synonym: F-actin / Oligomeric state: helical polymer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Tissue: muscle |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | GO: actin filament binding |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER |
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-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 |
Sample stage | Specimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 12.7 µm / Bits/pixel: 16 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 27.7 Å Applied symmetry - Helical parameters - Δ&Phi: 166.8 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IHRSR |
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