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Open data
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Basic information
Entry | Database: PDB / ID: 3lue | ||||||
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Title | Model of alpha-actinin CH1 bound to F-actin | ||||||
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![]() | STRUCTURAL PROTEIN / calponin homology domains / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Methylation / Nucleotide-binding / Phosphoprotein / Actin-binding / Calcium / Polymorphism / Deafness / Disease mutation / Dystonia | ||||||
Function / homology | ![]() 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 / cellular response to cytochalasin B / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / regulation of transepithelial transport ...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 / cellular response to cytochalasin B / positive regulation of skeletal muscle tissue growth / response to denervation involved in regulation of muscle adaptation / regulation of transepithelial transport / positive regulation of fast-twitch skeletal muscle fiber contraction / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / transition between fast and slow fiber / positive regulation of bone mineralization involved in bone maturation / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / muscle cell development / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / negative regulation of oxidative phosphorylation / focal adhesion assembly / Adherens junctions interactions / tight junction / Striated Muscle Contraction / bone morphogenesis / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / negative regulation of glycolytic process / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / negative regulation of cold-induced thermogenesis / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of calcineurin-NFAT signaling cascade / structural constituent of muscle / apical junction complex / regulation of aerobic respiration / establishment or maintenance of cell polarity / cortical actin cytoskeleton / regulation of cyclin-dependent protein serine/threonine kinase activity / cortical cytoskeleton / maintenance of blood-brain barrier / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / pseudopodium / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / kinesin binding / brush border / calyx of Held / negative regulation of cell differentiation / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / EPHB-mediated forward signaling / substantia nigra development / axonogenesis / negative regulation of protein binding / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity / adherens junction / FCGR3A-mediated phagocytosis / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / tau protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 15 Å | ||||||
![]() | Galkin, V.E. / Orlova, A. / Salmazo, A. / Djinovic-Carugo, K. / Egelman, E.H. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 824.1 KB | Display | ![]() |
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PDB format | ![]() | 640.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 861.1 KB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 184.5 KB | Display | |
Data in CIF | ![]() | 254.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5170MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Details | Authors state that the model is from a continuous helix where the rotation per subunit is -167.2 degrees and the rise per subunit is 26.6 Angstroms. |
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Components
#1: Protein | Mass: 41651.465 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 12471.712 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: gatan 626 / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Film or detector model: KODAK SO-163 FILM |
Image scans | Sampling size: 12.7 µm / Scanner model: NIKON COOLSCAN |
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Processing
EM software |
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CTF correction | Details: Weiner filter | ||||||||||||
Helical symmerty | Angular rotation/subunit: 166.8 ° / Axial rise/subunit: 27.7 Å / Axial symmetry: C1 | ||||||||||||
3D reconstruction | Method: back projection / Resolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF / Nominal pixel size: 2.38 Å / Actual pixel size: 2.38 Å Details: AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS. Symmetry type: HELICAL | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: METHOD--both manually and with Chimera DETAILS--AUTHORS STATE THAT THE STRANGE C-N BONDS WERE THE RESULT OF BREAKING THE CHAINS AT THESE POINTS TO DO RIGID BODY FITTING OF THE SUBDOMAINS. | ||||||||||||
Refinement step | Cycle: LAST
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