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- EMDB-16776: Human arginylated beta-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-16776
TitleHuman arginylated beta-actin
Map dataR-actin monomer map
Sample
  • Complex: Polymerised arginylated actin with bound ADP
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / methylated / filament / CONTRACTILE PROTEIN
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 / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / regulation of transepithelial transport / 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 / 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 / regulation of norepinephrine uptake / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / 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 / maintenance of blood-brain barrier / cortical cytoskeleton / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / nitric-oxide synthase binding / 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 / 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 / FCGR3A-mediated phagocytosis / adherens junction / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / 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 / Regulation of actin dynamics for phagocytic cup formation / kinetochore / cytoplasmic ribonucleoprotein granule / nuclear matrix / platelet aggregation / VEGFA-VEGFR2 Pathway / Signaling by RAF1 mutants / UCH proteinases / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / nucleosome / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin cytoskeleton / presynapse / lamellipodium / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / regulation of apoptotic process / vesicle
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
Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.499 Å
AuthorsPinto CS / Bakker SE / Suchenko A / Hussain H / Hatano T / Sampath K / Chinthalapudi K / Mishima M / Balasubramanian M
Funding support United Kingdom, European Union, 4 items
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 CS / Bakker SE / Suchenko A / Hussain H / Hatano T / Sampath K / Chinthalapudi K / Mishima M / Balasubramanian M
History
DepositionFeb 28, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16776.png

Downloads & links

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Map

FileDownload / File: emd_16776.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationR-actin monomer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0416
Minimum - Maximum-0.13820443 - 0.23095319
Average (Standard dev.)0.00015458181 (±0.0045420094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map 1

Fileemd_16776_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_16776_half_map_2.map
Annotationhalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polymerised arginylated actin with bound ADP

EntireName: Polymerised arginylated actin with bound ADP
Components
  • Complex: Polymerised arginylated actin with bound ADP
    • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Polymerised arginylated actin with bound ADP

SupramoleculeName: Polymerised arginylated actin with bound ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin, cytoplasmic 1, N-terminally processed

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.70659 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: RDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ...String:
RDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP EALFQPSFLG MESCGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 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.
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 60.0 sec. / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Used featureless cylinder as starting model for 3D classification.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.499 Å / Resolution method: FSC 0.143 CUT-OFF
Details: RELION 3.09 was used throughout using helical reconstruction.
Number images used: 42701
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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