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- PDB-7qep: Cryo-EM structure of the ribosome from Encephalitozoon cuniculi -

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Basic information

Entry
Database: PDB / ID: 7qep
TitleCryo-EM structure of the ribosome from Encephalitozoon cuniculi
Components
  • (40S RIBOSOMAL PROTEIN ...) x 28
  • (60S RIBOSOMAL PROTEIN ...) x 36
  • (Similarity to ...) x 2
  • 18S ribosomal RNA
  • 5.8S-23S ribosomal RNA
  • 5S ribosomal RNA
  • ECU06_1135 protein
  • ECU06_1215 protein
  • ECU11_0225 protein
  • Guanine nucleotide binding protein beta subunit
  • RIBOSOMAL PROTEIN S15
  • Ribosomal protein L15
  • UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION
  • Uncharacterized protein ECU01_0250
KeywordsRIBOSOME / genome decay / microbial parasite / genome reduction / Encephalitozoon cuniculi / lose-to-gain
Function / homology
Function and homology information


transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 90S preribosome / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / transcription initiation at RNA polymerase II promoter / modification-dependent protein catabolic process ...transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / 90S preribosome / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / transcription initiation at RNA polymerase II promoter / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal ...CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / Ribosomal L15/L27a, N-terminal / : / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / Plectin/S10, N-terminal / Ribosomal protein L10e, conserved site / Plectin/S10 domain / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein L13e / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal L40e family / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S19A/S15e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L39e, conserved site / Ribosomal protein L39e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / : / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein S6, eukaryotic / 60S ribosomal protein L19 / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S4e, N-terminal / Ribosomal protein L30/YlxQ / RS4NT (NUC023) domain / Ribosomal Protein L6, KOW domain / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / 60S ribosomal protein L35 / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / 60S ribosomal protein L6E / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein L37ae / Ribosomal protein S24e / Ribosomal L37ae protein family / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L36e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ECU06_1135 protein / 60S ribosomal protein L29 ...ADENOSINE MONOPHOSPHATE / SPERMIDINE / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / ECU06_1135 protein / 60S ribosomal protein L29 / ECU06_1215 protein / ECU11_0225 protein / Guanine nucleotide binding protein beta subunit / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL3 / 40S RIBOSOMAL PROTEIN S15A (S22 in yeast) / 40S RIBOSOMAL PROTEIN S28 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein eS19 / Ribosomal protein L15 / Small ribosomal subunit protein eS7 / 40S RIBOSOMAL PROTEIN S20 / 40S RIBOSOMAL PROTEIN S24 / Large ribosomal subunit protein eL42 / Small ribosomal subunit protein uS12 / 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN L6 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS4 / 60S RIBOSOMAL PROTEIN L4 / 60S ribosomal protein L20 / 60S RIBOSOMAL PROTEIN L26 / RIBOSOMAL PROTEIN S15 / 40S RIBOSOMAL PROTEIN S2 / Large ribosomal subunit protein eL37 / 60S RIBOSOMAL PROTEIN L17 / UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION / 60S RIBOSOMAL PROTEIN L37A (L43) / Small ribosomal subunit protein eS26 / Large ribosomal subunit protein eL36 / Small ribosomal subunit protein uS13 / 60S RIBOSOMAL PROTEIN L19 / 60S RIBOSOMAL PROTEIN L5 / 60S RIBOSOMAL PROTEIN L30 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS6 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein eS1 / 60S RIBOSOMAL PROTEIN L13A (L16) / 40S RIBOSOMAL PROTEIN S10 / Large ribosomal subunit protein eL32 / 40S RIBOSOMAL PROTEIN S27 / Large ribosomal subunit protein eL22 / 40S RIBOSOMAL PROTEIN S11 / Small ribosomal subunit protein uS2 / 60S RIBOSOMAL PROTEIN L27 / Small ribosomal subunit protein uS7 / 60S RIBOSOMAL PROTEIN L18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL34 / Small ribosomal subunit protein uS11 / 60S RIBOSOMAL PROTEIN L13 / 40S RIBOSOMAL PROTEIN S16 / Large ribosomal subunit protein eL31 / 60S RIBOSOMAL PROTEIN L35A (L33) / 60S RIBOSOMAL PROTEIN L9 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL5 / 40S RIBOSOMAL PROTEIN S12 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS25 / Similarity to 60S RIBOSOMAL PROTEIN L24 / Similarity to monoubiquitin/carboxy-extension protein fusion / 40S ribosomal protein S8 / Uncharacterized protein ECU01_0250
Similarity search - Component
Biological speciesEncephalitozoon cuniculi GB-M1 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsNicholson, D. / Ranson, N.A. / Melnikov, S.V.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
Wellcome Trust203743/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)G0901526 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
H2020 Marie Curie Actions of the European Commission97617 United Kingdom
H2020 Marie Curie Actions of the European Commission895166 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: 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
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
RA: Guanine nucleotide binding protein beta subunit
1: 5.8S-23S ribosomal RNA
2: 5S ribosomal RNA
3: 18S ribosomal RNA
C0: 40S RIBOSOMAL PROTEIN S10
C1: 40S RIBOSOMAL PROTEIN S11
C2: 40S RIBOSOMAL PROTEIN S12
C3: 40S ribosomal protein S13
C4: 40S ribosomal protein S14
C5: RIBOSOMAL PROTEIN S15
C6: 40S RIBOSOMAL PROTEIN S16
C7: 40S ribosomal protein S17
C8: 40S ribosomal protein S18
C9: 40S ribosomal protein S19
D0: 40S RIBOSOMAL PROTEIN S20
D1: ECU11_0225 protein
D2: 40S RIBOSOMAL PROTEIN S15A (S22 in yeast)
D3: 40S ribosomal protein S23
D4: 40S RIBOSOMAL PROTEIN S24
D5: 40S ribosomal protein S25
D6: 40S ribosomal protein S26
D7: 40S RIBOSOMAL PROTEIN S27
D8: 40S RIBOSOMAL PROTEIN S28
D9: 40S ribosomal protein S29
E1: Similarity to monoubiquitin/carboxy-extension protein fusion
L1: 60S ribosomal protein L1
L2: 60S ribosomal protein L8
L3: 60S ribosomal protein L3
L4: 60S RIBOSOMAL PROTEIN L4
L5: 60S RIBOSOMAL PROTEIN L5
L6: 60S RIBOSOMAL PROTEIN L6
L7: 60S ribosomal protein L7
L8: 60S ribosomal protein L7a
L9: 60S RIBOSOMAL PROTEIN L9
M0: 60S ribosomal protein L10
M1: 60S ribosomal protein L11
M3: 60S RIBOSOMAL PROTEIN L13
M4: ECU06_1215 protein
M5: Ribosomal protein L15
M6: 60S RIBOSOMAL PROTEIN L13A (L16)
M7: 60S RIBOSOMAL PROTEIN L17
M8: 60S RIBOSOMAL PROTEIN L18
M9: 60S RIBOSOMAL PROTEIN L19
MD: Uncharacterized protein ECU01_0250
MS: ECU06_1135 protein
N0: 60S ribosomal protein L20
N1: 60S ribosomal protein L21
N2: 60S ribosomal protein L22
N3: 60S ribosomal protein L23
N4: Similarity to 60S RIBOSOMAL PROTEIN L24
N5: 60S RIBOSOMAL PROTEIN L23A
N6: 60S RIBOSOMAL PROTEIN L26
N7: 60S RIBOSOMAL PROTEIN L27
N8: 60S ribosomal protein L27a
N9: 60S ribosomal protein L29
O0: 60S RIBOSOMAL PROTEIN L30
O1: 60S ribosomal protein L31
O2: 60S ribosomal protein L32
O3: 60S RIBOSOMAL PROTEIN L35A (L33)
O4: 60S ribosomal protein L34
O5: 60S ribosomal protein L35-1
O6: 60S ribosomal protein L36
O7: 60S ribosomal protein L37
O9: 60S ribosomal protein L39
P0: UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION
P2: 60S ribosomal protein L44
P3: 60S RIBOSOMAL PROTEIN L37A (L43)
S0: 40S ribosomal protein S0
S1: 40S ribosomal protein S1
S2: 40S RIBOSOMAL PROTEIN S2
S3: 40S ribosomal protein S3
S4: 40S ribosomal protein S4
S5: 40S ribosomal protein S5
S6: 40S ribosomal protein S6
S7: 40S ribosomal protein S7
S8: 40S ribosomal protein S8
S9: 40S ribosomal protein S9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,597,77287
Polymers2,596,75677
Non-polymers1,01610
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 8 types, 8 molecules RAC5D1M4M5MDMSP0

#1: Protein Guanine nucleotide binding protein beta subunit


Mass: 36828.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: M1K775
#10: Protein RIBOSOMAL PROTEIN S15


Mass: 16383.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRE7
#16: Protein ECU11_0225 protein


Mass: 7661.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: I7L8M6
#38: Protein ECU06_1215 protein


Mass: 12275.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: I7L8J2
#39: Protein Ribosomal protein L15


Mass: 23823.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQU2
#44: Protein Uncharacterized protein ECU01_0250


Mass: 19453.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SWQ4
#45: Protein ECU06_1135 protein


Mass: 9019.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: I7IV41
#65: Protein UBIQUITIN/ L40 RIBOSOMAL PROTEIN FUSION


Mass: 14312.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRH8

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RNA chain , 3 types, 3 molecules 123

#2: RNA chain 5.8S-23S ribosomal RNA


Mass: 807085.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: GenBank: 13560063
#3: RNA chain 5S ribosomal RNA


Mass: 38478.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: GenBank: 13560072
#4: RNA chain 18S ribosomal RNA


Mass: 422123.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: GenBank: 13560063

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40S RIBOSOMAL PROTEIN ... , 28 types, 28 molecules C0C1C2C3C4C6C7C8C9D0D2D3D4D5D6D7D8D9S0S1S2S3S4S5S6S7S8S9

#5: Protein 40S RIBOSOMAL PROTEIN S10


Mass: 11167.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS17
#6: Protein 40S RIBOSOMAL PROTEIN S11


Mass: 17788.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS53
#7: Protein 40S RIBOSOMAL PROTEIN S12


Mass: 14518.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSK9
#8: Protein 40S ribosomal protein S13


Mass: 16858.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRB3
#9: Protein 40S ribosomal protein S14


Mass: 14423.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSA6
#11: Protein 40S RIBOSOMAL PROTEIN S16


Mass: 16602.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSC2
#12: Protein 40S ribosomal protein S17


Mass: 14057.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSF9
#13: Protein 40S ribosomal protein S18


Mass: 17431.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRP2
#14: Protein 40S ribosomal protein S19


Mass: 15806.159 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQS8
#15: Protein 40S RIBOSOMAL PROTEIN S20


Mass: 14236.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQX6
#17: Protein 40S RIBOSOMAL PROTEIN S15A (S22 in yeast)


Mass: 14582.005 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQL9
#18: Protein 40S ribosomal protein S23


Mass: 15345.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR65
#19: Protein 40S RIBOSOMAL PROTEIN S24


Mass: 15529.335 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR06
#20: Protein 40S ribosomal protein S25


Mass: 12355.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8STD9
#21: Protein 40S ribosomal protein S26


Mass: 11902.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRN2
#22: Protein 40S RIBOSOMAL PROTEIN S27


Mass: 9434.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS34
#23: Protein 40S RIBOSOMAL PROTEIN S28


Mass: 7459.593 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQM2
#24: Protein 40S ribosomal protein S29


Mass: 7637.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1
#68: Protein 40S ribosomal protein S0


Mass: 27899.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS60
#69: Protein 40S ribosomal protein S1


Mass: 26985.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS05
#70: Protein 40S RIBOSOMAL PROTEIN S2


Mass: 26270.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRG6
#71: Protein 40S ribosomal protein S3


Mass: 24318.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQM3
#72: Protein 40S ribosomal protein S4


Mass: 30090.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRB9
#73: Protein 40S ribosomal protein S5


Mass: 20987.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS72
#74: Protein 40S ribosomal protein S6


Mass: 25518.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRY0
#75: Protein 40S ribosomal protein S7


Mass: 19032.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQX3
#76: Protein 40S ribosomal protein S8


Mass: 19615.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SWC9
#77: Protein 40S ribosomal protein S9


Mass: 20954.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRW6

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Similarity to ... , 2 types, 2 molecules E1N4

#25: Protein Similarity to monoubiquitin/carboxy-extension protein fusion


Mass: 17141.877 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SWB3
#50: Protein Similarity to 60S RIBOSOMAL PROTEIN L24


Mass: 11350.204 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SUZ9

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60S RIBOSOMAL PROTEIN ... , 36 types, 36 molecules L1L2L3L4L5L6L7L8L9M0M1M3M6M7M8M9N0N1N2N3N5N6N7N8N9O0O1O2O3O4...

#26: Protein 60S ribosomal protein L1 / L10a


Mass: 24752.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRY5
#27: Protein 60S ribosomal protein L8


Mass: 25911.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSM6
#28: Protein 60S ribosomal protein L3


Mass: 42555.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQI3
#29: Protein 60S RIBOSOMAL PROTEIN L4


Mass: 37767.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRC2
#30: Protein 60S RIBOSOMAL PROTEIN L5


Mass: 32770.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRQ3
#31: Protein 60S RIBOSOMAL PROTEIN L6


Mass: 19672.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR91
#32: Protein 60S ribosomal protein L7


Mass: 27987.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS93
#33: Protein 60S ribosomal protein L7a


Mass: 23587.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSG1
#34: Protein 60S RIBOSOMAL PROTEIN L9


Mass: 20649.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSF7
#35: Protein 60S ribosomal protein L10


Mass: 25047.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR96
#36: Protein 60S ribosomal protein L11


Mass: 19733.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSG9
#37: Protein 60S RIBOSOMAL PROTEIN L13


Mass: 18900.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSC1
#40: Protein 60S RIBOSOMAL PROTEIN L13A (L16)


Mass: 22724.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS16
#41: Protein 60S RIBOSOMAL PROTEIN L17


Mass: 20885.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRH7
#42: Protein 60S RIBOSOMAL PROTEIN L18


Mass: 22655.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS76
#43: Protein 60S RIBOSOMAL PROTEIN L19


Mass: 20198.928 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRP5
#46: Protein 60S ribosomal protein L20


Mass: 21592.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRD7
#47: Protein 60S ribosomal protein L21


Mass: 18621.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRW8
#48: Protein 60S ribosomal protein L22


Mass: 12598.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS49
#49: Protein 60S ribosomal protein L23


Mass: 16383.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRA7
#51: Protein 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN L23A (L25 in yeast)


Mass: 11839.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR87
#52: Protein 60S RIBOSOMAL PROTEIN L26


Mass: 16811.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRE6
#53: Protein 60S RIBOSOMAL PROTEIN L27


Mass: 14508.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS64
#54: Protein 60S ribosomal protein L27a


Mass: 17066.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: O62581
#55: Protein 60S ribosomal protein L29


Mass: 6565.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: I7JTZ6
#56: Protein 60S RIBOSOMAL PROTEIN L30


Mass: 11785.833 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRU1
#57: Protein 60S ribosomal protein L31


Mass: 13035.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSC8
#58: Protein 60S ribosomal protein L32


Mass: 16376.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SS18
#59: Protein 60S RIBOSOMAL PROTEIN L35A (L33)


Mass: 12832.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSF3
#60: Protein 60S ribosomal protein L34


Mass: 12463.718 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SSA2
#61: Protein 60S ribosomal protein L35-1


Mass: 14128.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8ST62
#62: Protein 60S ribosomal protein L36 / L39


Mass: 10776.858 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRP1
#63: Protein 60S ribosomal protein L37


Mass: 10416.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRH5
#64: Protein 60S ribosomal protein L39


Mass: 6517.931 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SQP8
#66: Protein 60S ribosomal protein L44


Mass: 12035.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SR18
#67: Protein 60S RIBOSOMAL PROTEIN L37A (L43)


Mass: 9849.786 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Encephalitozoon cuniculi GB-M1 (fungus) / Strain: GB-M1 / References: UniProt: Q8SRJ2

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Non-polymers , 3 types, 10 molecules

#78: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#79: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#80: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3

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Details

Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Ribosome from Encephalitozoon cuniculiRIBOSOME#1-#770NATURAL
2large subunitCOMPLEX#1-#2, #25-#42, #44-#661NATURAL
3small subunitCOMPLEX#3-#24, #67-#771NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Encephalitozoon cuniculi (fungus)6035strain II
32Encephalitozoon cuniculi (fungus)6035strain II
43Encephalitozoon cuniculi (fungus)6035strain II
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPES-KOH1
225 mMmagnesium chlorideMgCl21
3130 mMpotassium chlorideKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quorum GloQube, 10 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
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 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 magnification: 96000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.35 sec. / Electron dose: 60 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2210
Image scansWidth: 4096 / Height: 4096

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4RELION3.1CTF correction
5CTFFIND4.1CTF correction
8Coot0.9model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.14model refinement
Image processingDetails: 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles 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
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108005
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.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: correlation coefficient
Details: 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. ...Details: 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.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
14V88

4v88

14V881PDBexperimental model
26RM3

6rm3

16RM32PDBexperimental model
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0089177081
ELECTRON MICROSCOPYf_angle_d0.9431257068
ELECTRON MICROSCOPYf_chiral_restr0.052931606
ELECTRON MICROSCOPYf_plane_restr0.005818642
ELECTRON MICROSCOPYf_dihedral_angle_d20.590699220

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