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- PDB-8cog: Human arginylated beta-actin -

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Basic information

Entry
Database: PDB / ID: 8cog
TitleHuman arginylated beta-actin
ComponentsActin, cytoplasmic 1, N-terminally processed
KeywordsCONTRACTILE PROTEIN / actin / methylated / filament
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / 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 ...positive regulation of norepinephrine uptake / 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 / Tat protein binding / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / 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 / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / 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 / 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 / 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 / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / nuclear matrix / VEGFA-VEGFR2 Pathway / UCH proteinases / 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 / nucleosome / cell-cell junction / Signaling by BRAF and RAF1 fusions / actin cytoskeleton / presynapse / lamellipodium / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / blood microparticle / regulation of apoptotic process
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
ADENOSINE-5'-DIPHOSPHATE / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.499 Å
AuthorsPinto, 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
OrganizationGrant numberCountry
Wellcome TrustWT101885MA United Kingdom
European Research Council (ERC)671083-ACTOMYOSIN RINGEuropean Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003789/1 United Kingdom
Wellcome Trust203276/Z/16/Z United Kingdom
CitationJournal: 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
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Actin, cytoplasmic 1, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1583
Polymers41,7071
Non-polymers4522
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1000 Å2
ΔGint-19 kcal/mol
Surface area16660 Å2

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Components

#1: Protein Actin, cytoplasmic 1, N-terminally processed /


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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Polymerised arginylated actin with bound ADP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 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.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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

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Processing

SoftwareName: 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
EM software
IDNameVersionCategoryDetails
1RELION3.09particle selection
4RELIONCTF correction
7Cootmodel fitting
9REFMACmodel refinementServalcat
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 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
RefinementResolution: 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
RfactorNum. reflection% reflection
Rwork0.3599 28866 -
all0.36 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 77.447 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0133012
ELECTRON MICROSCOPYr_bond_other_d0.0010.0172823
ELECTRON MICROSCOPYr_angle_refined_deg1.6351.6484086
ELECTRON MICROSCOPYr_angle_other_deg1.3421.5766524
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.0485373
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.52822.109147
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.59415517
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.9071519
ELECTRON MICROSCOPYr_chiral_restr0.0710.2405
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.023368
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02662
ELECTRON MICROSCOPYr_nbd_refined0.210.21446
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1930.25716
ELECTRON MICROSCOPYr_nbtor_refined0.1660.22990
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0770.23152
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1550.2122
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.060.24
ELECTRON MICROSCOPYr_mcbond_it10.3477.2151494
ELECTRON MICROSCOPYr_mcbond_other10.3457.2151494
ELECTRON MICROSCOPYr_mcangle_it17.08810.8061866
ELECTRON MICROSCOPYr_mcangle_other17.08510.8191867
ELECTRON MICROSCOPYr_scbond_it12.8348.9541518
ELECTRON MICROSCOPYr_scbond_other12.8348.9541518
ELECTRON MICROSCOPYr_scangle_it21.72612.6972220
ELECTRON MICROSCOPYr_scangle_other21.72112.6932221
ELECTRON MICROSCOPYr_lrange_it36.106140.25312140
ELECTRON MICROSCOPYr_lrange_other36.105140.24312141
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.4-3.4881.03621231.03621230.491.036
3.488-3.5840.6520780.6520780.6070.65
3.584-3.6870.47620070.47620070.7010.476
3.687-3.8010.43819500.43819500.7420.438
3.801-3.9250.38418850.38418850.8060.384
3.925-4.0630.32818820.32818820.8570.328
4.063-4.2160.29918110.29918110.8910.299
4.216-4.3870.29916350.29916350.9150.299
4.387-4.5820.31316840.31316840.9330.313
4.582-4.8050.31715670.31715670.9410.317
4.805-5.0640.30514890.30514890.9420.305
5.064-5.370.29914210.29914210.9290.299
5.37-5.7390.28513320.28513320.9110.285
5.739-6.1970.28512470.28512470.8970.285
6.197-6.7850.30211330.30211330.8830.302
6.785-7.580.32510390.32510390.8760.325
7.58-8.7420.3078940.3078940.8730.307
8.742-10.6810.2637410.2637410.9050.263
10.681-14.9970.2616100.2616100.9420.261
14.997-88.560.7783380.7783380.9780.778

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