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- EMDB-18415: Cysteine tRNA ligase homodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-18415
TitleCysteine tRNA ligase homodimer
Map data
Sample
  • Complex: Homodimeric form of Cysteine tRNA ligase
    • Protein or peptide: Cysteine--tRNA ligase
  • Ligand: ZINC ION
Keywordscysteine / trna / ligase / synthetase / homodimer / RNA
Function / homology
Function and homology information


cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Cysteinyl-tRNA synthetase, class Ia, DALR / DALR domain / DALR_2 / Cysteine-tRNA ligase / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Cysteine--tRNA ligase
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsPacesa M / Correia BE / Levy ED
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Cell / Year: 2024
Title: An atlas of protein homo-oligomerization across domains of life.
Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / ...Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / Bruno E Correia / Sucharita Dey / Emmanuel D Levy /
Abstract: Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their ...Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
History
DepositionSep 8, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18415.png

Downloads & links

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Map

FileDownload / File: emd_18415.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 217.8 Å		0.73 Å/pix.
x 300 pix.
= 217.8 Å		0.73 Å/pix.
x 300 pix.
= 217.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.19041415 - 0.37065122
Average (Standard dev.)-0.0001398483 (±0.009754025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 217.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18415_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18415_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimeric form of Cysteine tRNA ligase

EntireName: Homodimeric form of Cysteine tRNA ligase
Components
  • Complex: Homodimeric form of Cysteine tRNA ligase
    • Protein or peptide: Cysteine--tRNA ligase
  • Ligand: ZINC ION

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Supramolecule #1: Homodimeric form of Cysteine tRNA ligase

SupramoleculeName: Homodimeric form of Cysteine tRNA ligase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 114 KDa

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Macromolecule #1: Cysteine--tRNA ligase

MacromoleculeName: Cysteine--tRNA ligase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus DSM 3638 (archaea)
Molecular weightTheoretical: 57.558605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHHHHHHGG SSGGLKVYNT LTKQKEEFKP LREGEVKMYV CGPTVYDYPH LGHARTYIAF DVIRRYLEHK GYTVLMVMNF TDIDDKIIK RARETGEDPK ELAERFIKIF LEDMEALKVK PADIYPRVTD HIDDIIEFIG KLKEKGYAYE GSDGIYFEVK K FPEYGKLS ...String:
MKHHHHHHGG SSGGLKVYNT LTKQKEEFKP LREGEVKMYV CGPTVYDYPH LGHARTYIAF DVIRRYLEHK GYTVLMVMNF TDIDDKIIK RARETGEDPK ELAERFIKIF LEDMEALKVK PADIYPRVTD HIDDIIEFIG KLKEKGYAYE GSDGIYFEVK K FPEYGKLS GVKIEDLQKG ARVEPGEGKK NPEDFALWKK AKPGEPKWDS PWGEGRPGWH IECSVMSSKY LGESFDIHGG GN DLIFPHH ENEIAQSEAC FGHEWVKYWL HTGFVMVKGE KMSKSLGNFV TIRELLKRYE PEVIRFFVLQ KHYRSPLEYT EEG LQHAKN NLQRLYNTLE NIRVALRNAE ISYTWGELEF KTYEIIREGK RKFYEAMDDD FNTAEALKAV FEVANAINKY LTEA NKPKE SILRKALEFF KIVSEVFGVF EDYFREETKE REESEKLIEL LVEVRKQLRK EKRYELADMI REELKKLGIQ LEDRG SETT WKRIIT

UniProtKB: Cysteine--tRNA ligase

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 186.0 K / Max: 192.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 60.0 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: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10059927
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 533971
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8qhp:
Cysteine tRNA ligase homodimer

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