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- PDB-8s8b: Phenylalanyl-tRNA Synthetase Domain Swap: evolutionary advantage? -

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Basic information

Entry
Database: PDB / ID: 8s8b
TitlePhenylalanyl-tRNA Synthetase Domain Swap: evolutionary advantage?
Components
  • Phenylalanyl-tRNA Synthetase alpha subunit
  • Phenylalanyl-tRNA Synthetase beta subunit
KeywordsRNA BINDING PROTEIN / Ligase Phenylalanine tRNA PheRS
Biological speciesCaenorhabditis tropicalis (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsReal-Hohn, A. / Ross, J.J. / Stefania, V. / Burga, A. / Dong, G.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP34880 Austria
CitationJournal: To Be Published
Title: Phenylalanyl-tRNA Synthetase Domain Swap: evolutionary advantage?
Authors: Real-Hohn, A. / Ross, J.J. / Stefania, V. / Burga, A. / Dong, G.
History
DepositionMar 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phenylalanyl-tRNA Synthetase alpha subunit
B: Phenylalanyl-tRNA Synthetase alpha subunit
C: Phenylalanyl-tRNA Synthetase beta subunit
D: Phenylalanyl-tRNA Synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,5366
Polymers245,4884
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "D"
d_2ens_2chain "C"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1LEULEULYSLYSAA185 - 496185 - 496
d_2ens_1LEULEULYSLYSBB185 - 496185 - 496
d_1ens_2PROPROLEULEUDD2 - 5902 - 590
d_2ens_2PROPROLEULEUCC2 - 5902 - 590

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999992612528, 0.00366169233073, -0.00116914401666), (-0.00365824636605, -0.999988998262, -0.00293608386829), (-0.00117988218982, -0.00293178516121, 0.999995006244)326.639845367, 328.170494405, 0.617161611587
2given(-0.999999999329, -1.16259974773E-5, 3.47277150406E-5), (1.16247904242E-5, -0.999999999328, -3.47576321979E-5), (3.47281191095E-5, -3.47572284721E-5, 0.999999998793)326.997227582, 327.00237392, -0.00286324510287

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Components

#1: Protein Phenylalanyl-tRNA Synthetase alpha subunit / Phenylalanine--tRNA ligase alpha subunit


Mass: 56155.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis tropicalis (invertebrata)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: phenylalanine-tRNA ligase
#2: Protein Phenylalanyl-tRNA Synthetase beta subunit / Phenylalanine--tRNA ligase beta subunit


Mass: 66588.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis tropicalis (invertebrata)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: phenylalanine-tRNA ligase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Phenylalanyl-tRNA Synthetase / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.244 MDa / Experimental value: YES
Source (natural)Organism: Caenorhabditis tropicalis (invertebrata)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMTrisTris-HCl1
2200 mMSodium ChlorideNaCl1
35 mMMagnesium DichlorideMgCl21
410 mM2-Mercaptoethanol2-ME1
55 % (v/v)GlycerolGlycerol1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Grids were blotted for 3 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2561

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Processing

EM software
IDNameVersionCategory
7PHENIX1.20.1model fitting
8Coot0.9.8.7model fitting
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 949918 / Details: 2D class template auto picker
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178962 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002714714
ELECTRON MICROSCOPYf_angle_d0.45819920
ELECTRON MICROSCOPYf_chiral_restr0.04262214
ELECTRON MICROSCOPYf_plane_restr0.00362580
ELECTRON MICROSCOPYf_dihedral_angle_d10.07445532
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints4.97441739463E-13
ens_2d_2DDELECTRON MICROSCOPYNCS constraints1.28941721118E-11

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