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- PDB-8v2o: Cryo-EM Structure of Wildtype Smooth Muscle Gamma Actin (ACTG2) -

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Basic information

Entry
Database: PDB / ID: 8v2o
TitleCryo-EM Structure of Wildtype Smooth Muscle Gamma Actin (ACTG2)
ComponentsActin, gamma-enteric smooth muscle
KeywordsSTRUCTURAL PROTEIN / Filament / Actin / Smooth Muscle / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


myosin filament / mesenchyme migration / Smooth Muscle Contraction / filopodium / cell periphery / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / blood microparticle / cytoskeleton ...myosin filament / mesenchyme migration / Smooth Muscle Contraction / filopodium / cell periphery / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lamellipodium / cell body / blood microparticle / cytoskeleton / hydrolase activity / positive regulation of gene expression / extracellular space / extracellular exosome / ATP binding / cytosol / cytoplasm
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, gamma-enteric smooth muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsPalmer, N.J. / Carman, P.J. / Ceron, R.H. / Dominguez, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: To Be Published
Title: Molecular Mechanisms of ACTG2 Mutations Linked to Visceral Myopathy
Authors: Ceron, R.H. / Baez-Cruz, F.A. / Palmer, N.J. / Carman, P.J. / Boczkowska, M. / Heuckeroth, R.O. / Ostap, E.M. / Dominguez, R.
History
DepositionNov 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin, gamma-enteric smooth muscle
B: Actin, gamma-enteric smooth muscle
C: Actin, gamma-enteric smooth muscle
D: Actin, gamma-enteric smooth muscle
E: Actin, gamma-enteric smooth muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,93715
Polymers209,6795
Non-polymers2,25810
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Actin, gamma-enteric smooth muscle / / Alpha-actin-3 / Gamma-2-actin / Smooth muscle gamma-actin / ACTG2


Mass: 41935.816 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Smooth Muscle / Gene: ACTG2, ACTA3, ACTL3, ACTSG / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
References: UniProt: P63267, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / 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.: 5 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Sequence detailsNumbering of the actin chains is shifted -1 from the medical ACTG2 literature to match the ...Numbering of the actin chains is shifted -1 from the medical ACTG2 literature to match the conventional numbering

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: ACTG2 filament / Type: COMPLEX / Details: ACTG2 filaments, purified from Expi293 cells / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: KILODALTONS/NANOMETER / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Tissue: Smooth
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 8 / Details: Actin F-buffer
Buffer component
IDConc.NameFormulaBuffer-ID
15 mMTrisNH2C(CH2OH)3(HCl)1
2100 mMPotassium ChlorideKCl1
30.2 mMCalcium chlorideCaCl21
41 mMEGTACH2OCH2CH2N(CH2CO2H)2]21
51 mMMagnesium ChlorideMgCl21
60.2 mMATPAdenosine triphosphateC10H14N5O13P3Na21
SpecimenConc.: 0.168 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: ACTG2 F-Actin in the ADP state.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot Force: 0 Blot Time: 2.5 s

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 526

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4particle selectionFilament tracer job
2EPUimage acquisition
4cryoSPARC4CTF correctionCTF correction job
7Coot0.9.8.3model fitting
12cryoSPARC43D reconstructionHelix Refinement
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.6 ° / Axial rise/subunit: 27.5 Å / Axial symmetry: C1
3D reconstructionResolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 473627 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414985
ELECTRON MICROSCOPYf_angle_d0.77920340
ELECTRON MICROSCOPYf_dihedral_angle_d6.2832090
ELECTRON MICROSCOPYf_chiral_restr0.0482250
ELECTRON MICROSCOPYf_plane_restr0.0092605

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