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- EMDB-19800: Phenylalanyl-tRNA Synthetase from Caenorhabditis tropicalis -

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Basic information

Entry
Database: EMDB / ID: EMD-19800
TitlePhenylalanyl-tRNA Synthetase from Caenorhabditis tropicalis
Map data178962 C2
Sample
  • Complex: Phenylalanyl-tRNA Synthetase
    • Protein or peptide: Phenylalanyl-tRNA Synthetase alpha subunit
    • Protein or peptide: Phenylalanyl-tRNA Synthetase beta subunit
  • Ligand: MAGNESIUM ION
KeywordsLigase Phenylalanine tRNA PheRS / RNA BINDING PROTEIN
Biological speciesCaenorhabditis tropicalis (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsReal-Hohn A / Ross JJ / Stefania V / Burga A / Dong G
Funding support Austria, 1 items
OrganizationGrant numberCountry
Austrian Science FundP34880 Austria
CitationJournal: To Be Published
Title: Phenylalanyl-tRNA Synthetase Domain Swap: evolutionary advantage?
Authors: Real-Hohn A / Ross JJ / Stefania V / Burga A / Dong G
History
DepositionMar 6, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19800.png

Downloads & links

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Map

FileDownload / File: emd_19800.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation178962 C2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.588
Minimum - Maximum-1.5852406 - 3.2114413
Average (Standard dev.)-0.00036130648 (±0.07022858)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19800_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19800_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Phenylalanyl-tRNA Synthetase

EntireName: Phenylalanyl-tRNA Synthetase
Components
  • Complex: Phenylalanyl-tRNA Synthetase
    • Protein or peptide: Phenylalanyl-tRNA Synthetase alpha subunit
    • Protein or peptide: Phenylalanyl-tRNA Synthetase beta subunit
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Phenylalanyl-tRNA Synthetase

SupramoleculeName: Phenylalanyl-tRNA Synthetase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Caenorhabditis tropicalis (invertebrata)
Molecular weightTheoretical: 244 KDa

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Macromolecule #1: Phenylalanyl-tRNA Synthetase alpha subunit

MacromoleculeName: Phenylalanyl-tRNA Synthetase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phenylalanine-tRNA ligase
Source (natural)Organism: Caenorhabditis tropicalis (invertebrata)
Molecular weightTheoretical: 56.155531 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MTAETAARTT DNLPQQVLDF LDNSNEFNTI QLAQEWNVDH QRLIGAIKSL LANEGVLATK DVTEKRLELT NEGVQFANEG SPEFLVFQF VGADGAAQAD IQKQPFGKIG MSKAMQFKWV SVDKGRVVRQ TAEVVDSTRK QLESLRLGSD DVNENEKKEL K KRKLISEV ...String:
MTAETAARTT DNLPQQVLDF LDNSNEFNTI QLAQEWNVDH QRLIGAIKSL LANEGVLATK DVTEKRLELT NEGVQFANEG SPEFLVFQF VGADGAAQAD IQKQPFGKIG MSKAMQFKWV SVDKGRVVRQ TAEVVDSTRK QLESLRLGSD DVNENEKKEL K KRKLISEV NIKGLVVSKG SSFTTSLAKQ EADLTPEMIA SGSWKEKQFK KYNFESLGVV PSSGHLHPLM KVRSEFRQIF FS MGFSEMA TNRYVESSFW NFDALFQPQQ HPARDAHDTF FVSDPAISVK FPEDYLERVK TVHSKGGYGS AGYNYDWKIE EAQ KNVLRT HTTAVSARQL YQLAQEGFRP SKLFSIDRVF RNETLDATHL AEFHQVEGVI AEKNLSLAHL IGIFTEFFKK LGIT DLRFK PTYNPYTEPS MEIFAYHKGL AKWVEIGNSG MFRPEMLLPM GLPADVNVAG YGLSLERPTM IKYGINNIRD LFGSK IDLE VVYNNPICRL DK

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Macromolecule #2: Phenylalanyl-tRNA Synthetase beta subunit

MacromoleculeName: Phenylalanyl-tRNA Synthetase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: phenylalanine-tRNA ligase
Source (natural)Organism: Caenorhabditis tropicalis (invertebrata)
Molecular weightTheoretical: 66.588312 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPTVGIKKVL LDKHFGRVYT EKEFDELCFE YGLELDEITS EKAAVEKERG EAAAGEDLND QEVYKIDIPA NRYDLLSVEG LSRAIRIFK QEIESPEYRF SDTKTRQKII VKRETAQVRP YVVGAVLRDV SFDSDSYASF IDLQDKLHQN ICRKRTLVAI G THDLDTIQ ...String:
MPTVGIKKVL LDKHFGRVYT EKEFDELCFE YGLELDEITS EKAAVEKERG EAAAGEDLND QEVYKIDIPA NRYDLLSVEG LSRAIRIFK QEIESPEYRF SDTKTRQKII VKRETAQVRP YVVGAVLRDV SFDSDSYASF IDLQDKLHQN ICRKRTLVAI G THDLDTIQ GPFEYRAEAP NKIKFRPLNQ TKEYTAEELM TLYSTDSHLK AYLPIIQNHP VYPVIYDKNG VVCSMPPIIN GE HSKITLK TKNVFIEATA TDKQKAYVVL DTIVTLFSQY CQKPFHVEQV EVEYEETGEK ELYPLLSYRE MTVTTPEINT KIG LSLKDE EMAILLNKMS LKAEVASKGV LKVVVPPTRH DILHACDIAE DVGVAYGYNN LVTKLPESNT VAVAFPINKL CDNL RIEIA AAGWTEALNF ALCSRDDIST KLRLPDALSK AVHIGNPKTL EFQVARTSLL PGLLKTLASN RDMPLPLKLF ELQDV ILKD EKMDVGARNE RRLAAVYYNK AAGFEIIQGF LDRMMRMLNV NPTKDQKGYH IEADENPTFF PGRCARIIGP NGVFLG RIG ALHPEVITSF GLTLPCGAVE FNVEPFL

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / 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 stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
40.0 mMTris-HClTris
200.0 mMNaClSodium Chloride
5.0 mMMgCl2Magnesium Dichloride
10.0 mM2-ME2-Mercaptoethanol
5.0 % (v/v)GlycerolGlycerol
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: Grids were blotted for 3 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 2561 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
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

Particle selectionNumber selected: 949918 / Details: 2D class template auto picker
Startup modelType of model: OTHER / Details: Ab initio reconstruction (C1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178962
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 300000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

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

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