EMDB-16776: Human arginylated beta-actin

Basic information

Entry

Database: EMDB / ID: EMD-16776

• Title: Human arginylated beta-actin
• Map data: R-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

• Keywords: actin / methylated / filament / CONTRACTILE PROTEIN

Function / homology

Function:

positive regulation of norepinephrine uptake / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / regulation of transepithelial transport / Formation of the canonical BAF (cBAF) complex / morphogenesis of a polarized epithelium / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / Formation of the polybromo-BAF (pBAF) complex / Gap junction degradation / GBP-mediated host defense / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / protein localization to adherens junction / Formation of the non-canonical BAF (ncBAF) complex / Cell-extracellular matrix interactions / regulation of G0 to G1 transition / dense body / Folding of actin by CCT/TriC / Tat protein binding / postsynaptic actin cytoskeleton / Regulation of CDH1 Function / apical protein localization / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / regulation of double-strand break repair / microtubule nucleation / adherens junction assembly / RHOF GTPase cycle / Sensory processing of sound by outer hair cells of the cochlea / tight junction / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / maintenance of blood-brain barrier / Interaction between L1 and Ankyrins / apical junction complex / regulation of nucleotide-excision repair / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / regulation of norepinephrine uptake / transporter regulator activity / Recycling pathway of L1 / cortical cytoskeleton / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / negative regulation of cell differentiation / establishment or maintenance of cell polarity / nitric-oxide synthase binding / brush border / EPH-ephrin mediated repulsion of cells / positive regulation of myoblast differentiation / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / kinesin binding / regulation of protein localization to plasma membrane / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of G1/S transition of mitotic cell cycle / axonogenesis / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / cell motility / nitric-oxide synthase regulator activity / FCGR3A-mediated phagocytosis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / positive regulation of cell differentiation / adherens junction / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / VEGFA-VEGFR2 Pathway / B-WICH complex positively regulates rRNA expression / tau protein binding / Schaffer collateral - CA1 synapse / DNA Damage Recognition in GG-NER / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / nuclear matrix / Signaling by RAF1 mutants / cell-cell junction / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin cytoskeleton / Signaling by BRAF and RAF1 fusions / UCH proteinases / lamellipodium / presynapse / HATs acetylate histones / Clathrin-mediated endocytosis / Factors involved in megakaryocyte development and platelet production

Domain/homology:

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

Component:

Actin, cytoplasmic 1

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / cryo EM / Resolution: 3.499 Å
• Authors: Pinto 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

Organization	Grant number	Country
Wellcome Trust	WT101885MA	United Kingdom
European Research Council (ERC)	671083-ACTOMYOSIN RING	European Union
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/S003789/1	United Kingdom
Wellcome Trust	203276/Z/16/Z	United Kingdom

• Citation: Journal: J Cell Biol / Year: 2026; Title: Actin arginylation alters myosin engagement and F-actin patterning despite structural conservation.; Authors: Clyde Savio Pinto / Saskia E Bakker / Andrejus Suchenko / Isabella M Kolodny / Hamdi Hussain / Tomoyuki Hatano / Karuna Sampath / Krishna Chinthalapudi / Sarah M Heissler / Masanori Mishima / Mohan Balasubramanian / ; Abstract: Actin is a conserved protein with crucial roles in cell polarity, division, and muscle contraction. Its function is regulated in part by posttranslational modifications, one of which is N-terminal arginylation. What is the structure of arginylated-β-actin (R-β-actin), and how does it regulate F-actin function? Here we report the 3.6 Å structures of ADP-R-β-actin filaments, which are nearly identical to that of non-arginylated F-actin. In vitro assays reveal that the interaction between myosin-II and actin is altered upon actin arginylation, characterized by frequent detachment of R-actin filaments from myosin-II. In vivo, replacement of the only actin gene in Schizosaccharomyces pombe with a synthetic gene encoding R-Sp-actin reduces Arp2/3-based actin patches while thickening formin-induced actin cables. Consistent with defective interactions between myosin-II and R-actin filaments, assembly and constriction of the cytokinetic actomyosin ring are perturbed in R-Sp-actin cells. Thus, despite structural similarity of arginylated and non-arginylated actin filaments, actin arginylation affects F-actin assortment into distinct subcellular structures and its interaction with myosin-II.

History

Deposition	Feb 28, 2023	-
Header (metadata) release	Mar 6, 2024	-
Map release	Mar 6, 2024	-
Update	Dec 17, 2025	-
Current status	Dec 17, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_16776.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: R-actin monomer map
• Voxel size: X=Y=Z: 1.08 Å

Density

Contour Level	By AUTHOR: 0.0416
Minimum - Maximum	-0.13820443 - 0.23095319
Average (Standard dev.)	0.00015458181 (±0.0045420094)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 276.48 Å α=β=γ: 90.0 °

Supplemental data

Half map: half-map 1

• File: emd_16776_half_map_1.map
• Annotation: half-map 1

Half map: half-map 2

• File: emd_16776_half_map_2.map
• Annotation: half-map 2

Sample components

Entire : Polymerised arginylated actin with bound ADP

• Entire: Name: 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

Supramolecule #1: Polymerised arginylated actin with bound ADP

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

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

• Macromolecule: Name: 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 weight: Theoretical: 41.70659 KDa
• Recombinant expression: Organism: Komagataella pastoris (fungus)

Sequence

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

Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

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

Macromolecule #3: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: helical array

Sample preparation

• Buffer: 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.
• Grid: Model: 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
• Vitrification: Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Image recording: Film 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/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 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 stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: OTHER; Details: Used featureless cylinder as starting model for 3D classification.
• Final reconstruction: Algorithm: 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 assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD