+Open data
-Basic information
Entry | Database: PDB / ID: 8cog | |||||||||||||||
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Title | Human arginylated beta-actin | |||||||||||||||
Components | Actin, cytoplasmic 1, N-terminally processed | |||||||||||||||
Keywords | CONTRACTILE PROTEIN / actin / methylated / filament | |||||||||||||||
Function / homology | Function and homology information positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / brahma complex / nBAF complex / protein localization to adherens junction / postsynaptic actin cytoskeleton / Tat protein binding / structural constituent of postsynaptic actin cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / GBAF complex / dense body / regulation of G0 to G1 transition / Formation of annular gap junctions / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of norepinephrine uptake / Interaction between L1 and Ankyrins / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / apical junction complex / establishment or maintenance of cell polarity / 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 / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / 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 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / adherens junction / FCGR3A-mediated phagocytosis / regulation of transmembrane transporter activity / 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 / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / 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 / UCH proteinases / Signaling by BRAF and RAF1 fusions / nucleosome / cell-cell junction / actin cytoskeleton / lamellipodium / presynapse / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / regulation of apoptotic process Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.499 Å | |||||||||||||||
Authors | Pinto, C.S. / Bakker, S.E. / Suchenko, A. / Hussain, H. / Hatano, T. / Sampath, K. / Chinthalapudi, K. / Mishima, M. / Balasubramanian, M. | |||||||||||||||
Funding support | United Kingdom, European Union, 4items
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Citation | Journal: To Be Published Title: Structure and physiological investigation of human arginylated beta-actin Authors: Pinto, C.S. / Bakker, S.E. / Suchenko, A. / Hussain, H. / Hatano, T. / Sampath, K. / Chinthalapudi, K. / Mishima, M. / Balasubramanian, M. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cog.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cog.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 8cog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cog_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8cog_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8cog_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 8cog_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/8cog ftp://data.pdbj.org/pub/pdb/validation_reports/co/8cog | HTTPS FTP |
-Related structure data
Related structure data | 16776MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 41706.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Komagataella pastoris (fungus) / References: UniProt: P60709 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Polymerised arginylated actin with bound ADP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Komagataella pastoris (fungus) |
Buffer solution | pH: 7.4 Details: Actin for EM was polymerized by mixing, 20 ul 20 uM G-actin, 8 ul 10x MKE and 52 ul 5 mM HEPES-KOH pH 7.4 containing 0.2 mM ATP and 0.5 mM DTT and incubating at RT for 1 hour. |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 60 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
Software | Name: REFMAC / Version: 5.8.0267 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: 2020-24-08 Description: (un)restrained refinement or idealisation of macromolecular structures | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.499 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42701 / Algorithm: FOURIER SPACE Details: RELION 3.09 was used throughout using helical reconstruction. Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.499→3.499 Å / Cor.coef. Fo:Fc: 0.806 / WRfactor Rwork: 0.36 / SU B: 20.983 / SU ML: 0.319 / Average fsc overall: 0.8232 / Average fsc work: 0.8232 / ESU R: 0.508 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.447 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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