- EMDB-13936: Cryo-EM structure of the ribosome from Encephalitozoon cuniculi -
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Basic information
Entry
Database: EMDB / ID: EMD-13936
Title
Cryo-EM structure of the ribosome from Encephalitozoon cuniculi
Map data
consensus map
Sample
Complex: Ribosome from Encephalitozoon cuniculi
Complex: large subunit
Protein or peptide: x 42 types
RNA: x 1 types
Complex: small subunit
RNA: x 2 types
Protein or peptide: x 31 types
Protein or peptide: x 1 types
Ligand: x 3 types
Function / homology
Function and homology information
rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome ...rRNA processing / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / nucleolus / RNA binding / nucleus / metal ion binding / cytoplasm Similarity search - Function
CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic ...CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / Ribosomal protein L30e / Ribosomal L15/L27a, N-terminal / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal L29e protein family / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L1 / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S19A/S15e / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal L40e family / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S6, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / 60S ribosomal protein L19 / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein L30/YlxQ / Ribosomal protein S27 / Ribosomal Protein L6, KOW domain / Ribosomal protein S8e / Ribosomal protein L13, eukaryotic/archaeal / Ribosomal protein L7A/L8 / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein L6e / Ribosomal protein S28e / Ribosomal protein S28e / 60S ribosomal protein L6E / Ribosomal protein S6e / Ribosomal protein L18e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein L37ae Similarity search - Domain/homology
ECU06_1135 protein / 60S ribosomal protein L29 / ECU06_1215 protein / ECU11_0225 protein / Guanine nucleotide binding protein beta subunit / 60S ribosomal protein L27a / 60S ribosomal protein L3 / 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) / 40S RIBOSOMAL PROTEIN S28 / 40S ribosomal protein S3 ...ECU06_1135 protein / 60S ribosomal protein L29 / ECU06_1215 protein / ECU11_0225 protein / Guanine nucleotide binding protein beta subunit / 60S ribosomal protein L27a / 60S ribosomal protein L3 / 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) / 40S RIBOSOMAL PROTEIN S28 / 40S ribosomal protein S3 / 60S ribosomal protein L39 / 40S ribosomal protein S19 / Ribosomal protein L15 / 40S ribosomal protein S7 / 40S RIBOSOMAL PROTEIN S20 / 40S RIBOSOMAL PROTEIN S24 / 60S ribosomal protein L44 / 40S ribosomal protein S23 / 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN L6 / 60S ribosomal protein L10 / 60S ribosomal protein L23 / 40S ribosomal protein S13 / 40S ribosomal protein S4 / 60S RIBOSOMAL PROTEIN L4 / 60S ribosomal protein L20 / 60S RIBOSOMAL PROTEIN L26 / RIBOSOMAL PROTEIN S15 / 40S RIBOSOMAL PROTEIN S2 / 60S ribosomal protein L37 / 60S RIBOSOMAL PROTEIN L17 / UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION / 60S RIBOSOMAL PROTEIN L37A (L43) / 40S ribosomal protein S26 / 60S ribosomal protein L36 / 40S ribosomal protein S18 / 60S RIBOSOMAL PROTEIN L19 / 60S RIBOSOMAL PROTEIN L5 / 60S RIBOSOMAL PROTEIN L30 / 40S ribosomal protein S9 / 60S ribosomal protein L21 / 40S ribosomal protein S6 / 60S ribosomal protein L1 / 40S ribosomal protein S1 / 60S RIBOSOMAL PROTEIN L13A (L16) / 40S RIBOSOMAL PROTEIN S10 / 60S ribosomal protein L32 / 40S RIBOSOMAL PROTEIN S27 / 60S ribosomal protein L22 / 40S RIBOSOMAL PROTEIN S11 / 40S ribosomal protein S0 / 60S RIBOSOMAL PROTEIN L27 / 40S ribosomal protein S5 / 60S RIBOSOMAL PROTEIN L18 / 60S ribosomal protein L7 / 60S ribosomal protein L34 / 40S ribosomal protein S14 / 60S RIBOSOMAL PROTEIN L13 / 40S RIBOSOMAL PROTEIN S16 / 60S ribosomal protein L31 / 60S RIBOSOMAL PROTEIN L35A (L33) / 60S RIBOSOMAL PROTEIN L9 / 40S ribosomal protein S17 / 60S ribosomal protein L7a / 60S ribosomal protein L11 / 40S RIBOSOMAL PROTEIN S12 / 60S ribosomal protein L8 / 60S ribosomal protein L35-1 / 40S ribosomal protein S25 / Similarity to 60S RIBOSOMAL PROTEIN L24 / Similarity to monoubiquitin/carboxy-extension protein fusion / 40S ribosomal protein S8 / Uncharacterized protein ECU01_0250 Similarity search - Component
H2020 Marie Curie Actions of the European Commission
97617
United Kingdom
H2020 Marie Curie Actions of the European Commission
895166
United Kingdom
Wellcome Trust
108466/Z/15/Z
United Kingdom
Citation
Journal: Nat Commun / Year: 2022 Title: Adaptation to genome decay in the structure of the smallest eukaryotic ribosome. Authors: David Nicholson / Marco Salamina / Johan Panek / Karla Helena-Bueno / Charlotte R Brown / Robert P Hirt / Neil A Ranson / Sergey V Melnikov / Abstract: The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious ...The evolution of microbial parasites involves the counterplay between natural selection forcing parasites to improve and genetic drifts forcing parasites to lose genes and accumulate deleterious mutations. Here, to understand how this counterplay occurs at the scale of individual macromolecules, we describe cryo-EM structure of ribosomes from Encephalitozoon cuniculi, a eukaryote with one of the smallest genomes in nature. The extreme rRNA reduction in E. cuniculi ribosomes is accompanied with unparalleled structural changes, such as the evolution of previously unknown molten rRNA linkers and bulgeless rRNA. Furthermore, E. cuniculi ribosomes withstand the loss of rRNA and protein segments by evolving an ability to use small molecules as structural mimics of degenerated rRNA and protein segments. Overall, we show that the molecular structures long viewed as reduced, degenerated, and suffering from debilitating mutations possess an array of compensatory mechanisms that allow them to remain active despite the extreme molecular reduction.
History
Deposition
Dec 3, 2021
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Header (metadata) release
Feb 9, 2022
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Map release
Feb 9, 2022
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Update
Feb 9, 2022
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Current status
Feb 9, 2022
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Quorum GloQube, 10 mA
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Quantifoil grids (R1.2/1.3, 400 mesh, copper) were glow discharged (10 mA, 30s, Quorum GloQube), and 3 microlitres of the crude sample of E. cuniculi ribosomes (300 nM) was pipetted onto a ...Details: Quantifoil grids (R1.2/1.3, 400 mesh, copper) were glow discharged (10 mA, 30s, Quorum GloQube), and 3 microlitres of the crude sample of E. cuniculi ribosomes (300 nM) was pipetted onto a grid. Excess sample was immediately blotted off and vitrification was performed by plunging the grid into liquid nitrogen-cooled liquid ethane at 100% humidity and 4 degrees celsius using an FEI Vitrobot Mark IV (Thermo Fisher).
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 2210 / Average exposure time: 1.35 sec. / Average electron dose: 60.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Drift-corrected and dose-corrected averages of each movie were created using RELION 3.1s own implementation of motion correction and the contrast transfer functions estimated using CTFFIND-4.1
Particle selection
Number selected: 260895 Details: Particles were picked using Laplacian-of-Gaussian autopicking and reference-free 2D classification used to generate templates for further autopicking. The resulting particles were extracted ...Details: Particles were picked using Laplacian-of-Gaussian autopicking and reference-free 2D classification used to generate templates for further autopicking. The resulting particles were extracted with binning-by-4, and 2D and 3D classification performed to remove junk images
Type of model: INSILICO MODEL In silico model: The 3D classification step was carried out using a 60 Angstroms low-passed filtered ab initio starting model made using a stochastic gradient descent procedure.
Final reconstruction
Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) Details: The remaining particles were re-extracted without binning and aligned and refined in 3D, again using a 60 Angstrom low-passed filtered ab initio starting model. Rounds of CTF refinement and ...Details: The remaining particles were re-extracted without binning and aligned and refined in 3D, again using a 60 Angstrom low-passed filtered ab initio starting model. Rounds of CTF refinement and Bayesian polishing were performed until the map resolution stopped improving. 108,005 particles fed into the final 3D reconstruction of estimated resolution 2.7 Angstrom. Number images used: 108005
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
The model was built using fragments of S. cerevisiae (pdb id 4v88) and V. necatrix ribosomes (pdb id 6rm3) as starting models that were edited using Coot using genomic sequences of the E. cuniculi strain GB-M1 to model rRNA and ribosomal proteins. For ribosomal proteins that are encoded by two alternative genes (with one gene coding for a zinc-coordinating protein and another gene coding for a zinc-free ribosomal protein), we used zinc-coordinating isoforms, because the cryo-EM map revealed the presence of these isoforms and not their zinc-free paralogs in the ribosome structure. The identity of protein msL2 in the ribosome structure was determined using the genomic sequence of the E. cuniculi strain GB-M1 and the cryo-EM map that revealed a unique combination of aromatic and bulky amino acids in its structure: the cryo-EM map showed that msL2 has a tyrosine residue at position 5, a tryptophan residue at position 9, and lysine or arginine residues at positions 10, 12 and 13. The only protein with this sequence was the hypothetical protein ECU06_1135, whose sequence and length were fully consistent with the cryo-EM map. The structure of E. cuniculi ribosomes was refined using Phenix real space refine and validated using MolProbity within Phenix and PDB OneDep. The parts of the model corresponding to the 60S, 40S body and 40S head were built and refined using the consensus map, 40S body multibody map and 40S head multibody map, respectively.
Refinement
Space: REAL / Protocol: OTHER / Target criteria: correlation coefficient
Output model
PDB-7qep: Cryo-EM structure of the ribosome from Encephalitozoon cuniculi
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