+Open data
-Basic information
Entry | Database: PDB / ID: 3lue | ||||||
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Title | Model of alpha-actinin CH1 bound to F-actin | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / calponin homology domains / Acetylation / ATP-binding / Cytoplasm / Cytoskeleton / Methylation / Nucleotide-binding / Phosphoprotein / Actin-binding / Calcium / Polymorphism / Deafness / Disease mutation / Dystonia | ||||||
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 / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of glycolytic process / SWI/SNF complex / Interaction between L1 and Ankyrins / 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 / cell motility / actin filament / 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 | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 15 Å | ||||||
Authors | Galkin, V.E. / Orlova, A. / Salmazo, A. / Djinovic-Carugo, K. / Egelman, E.H. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3lue.cif.gz | 824.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lue.ent.gz | 640.8 KB | Display | PDB format |
PDBx/mmJSON format | 3lue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/3lue ftp://data.pdbj.org/pub/pdb/validation_reports/lu/3lue | HTTPS FTP |
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-Related structure data
Related structure data | 5170MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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. |
-Components
#1: Protein | Mass: 41651.465 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Escherichia coli (E. coli) / References: UniProt: P60709 #2: Protein | Mass: 12471.712 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08043 |
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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 |
-Sample preparation
Component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
-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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