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- PDB-8p5d: Spraguea lophii ribosome in the closed conformation by cryo sub t... -

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Basic information

Entry
Database: PDB / ID: 8p5d
TitleSpraguea lophii ribosome in the closed conformation by cryo sub tomogram averaging
Components
  • (40S ribosomal protein ...) x 23
  • (60S ribosomal protein ...) x 27
  • (Ribosomal protein ...) x 7
  • DNL-type domain-containing protein
  • Guanine nucleotide binding protein beta subunit
  • RNA 16S
  • RNA 28S
  • RNA 5S
  • Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein
  • S60 ribosomal protein L10
  • Transposase
  • Ubiquitin
  • Ubiquitin/40s ribosomal protein S27a fusion
  • eL37
  • eS1
  • eS17
  • eS27
  • eS28
  • eS30
  • uL15
  • uS12
KeywordsRIBOSOME / Microsporidia
Function / homology
Function and homology information


90S preribosome / translation regulator activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity ...90S preribosome / translation regulator activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase C binding / modification-dependent protein catabolic process / protein tag activity / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome binding / 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 / positive regulation of protein phosphorylation / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / : / 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 S21e ...CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / : / 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 S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein L22e / Ribosomal protein L22e superfamily / S27a-like superfamily / Ribosomal L22e protein family / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / 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 S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / 60S ribosomal protein L18a/ L20, eukaryotes / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / 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 / 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 protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal_L40e / Ribosomal protein L40e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L40e superfamily / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / : / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L19 / Ribosomal protein S4e, N-terminal / Ribosomal protein L30/YlxQ / RS4NT (NUC023) domain / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / 60S ribosomal protein L6E / 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 L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein S8e / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L35A superfamily / Ribosomal protein L32e, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / Uncharacterized protein / 60S ribosomal protein L6 / 60S ribosomal protein L35a / 40S ribosomal protein S14 / 60S ribosomal protein L37a ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / Uncharacterized protein / 60S ribosomal protein L6 / 60S ribosomal protein L35a / 40S ribosomal protein S14 / 60S ribosomal protein L37a / 60S ribosomal protein L8 / Ribosomal protein L15 / Ribosomal protein L34 / 40S ribosomal protein S12 / 40S Ribosomal protein S19 / 40S ribosomal protein S2 / Ribosomal L29 protein / 60S ribosomal protein L26 / 40S ribosomal protein S9 / 60s ribosomal protein L21 / 40s ribosomal protein s24 / 40S ribosomal protein S11 / 40S ribosomal protein S0 / 60S ribosomal protein L7 / Large ribosomal subunit protein eL22 / 40S ribosomal protein S20 / 40S ribosomal protein S26 / Ubiquitin/40s ribosomal protein S27a fusion / Ribosomal protein S21E / 60S ribosomal protein L20 / 60S ribosomal protein L18 / 40S ribosomal protein S25 / 40S ribosomal protein S3 / 60S ribosomal protein L3 / 60S ribosomal protein L11 / S60 ribosomal protein L10 / 60S ribosomal protein L19 / 60S ribosomal protein L4 / 40S ribosomal protein S6 / 60S ribosomal protein L17 / 40S ribosomal protein S16 / 60S ribosomal protein L36 / 60S ribosomal protein L3 / 60S ribosomal protein L23a / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 60S ribosomal protein L5 / 40S ribosomal protein S18 / 40S ribosomal protein S29 / 40S ribosomal protein S15A / 60S ribosomal protein L32 / Ribosomal protein S19 / 60S ribosomal protein L44 / Ribosomal protein L23 / 60S ribosomal protein L9 / Ubiquitin / Ribosomal protein L24E / 60S ribosomal protein L39 / 60S ribosomal protein L27 / 40S ribosomal protein S10 / 60S ribosomal protein L8 / Ribosomal protein L13A / 40S ribosomal protein S7 / Guanine nucleotide binding protein beta subunit / 60S ribosomal protein L13 / Uncharacterized protein / 40S ribosomal protein S13 / 60S ribosomal protein L31
Similarity search - Component
Biological speciesSpraguea lophii 42_110 (fungus)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 10.8 Å
AuthorsGil Diez, P. / McLaren, M. / Isupov, M.N. / Daum, B. / Conners, R. / Williams, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust212439/Z/18/Z United Kingdom
CitationJournal: Nat Microbiol / Year: 2023
Title: CryoEM reveals that ribosomes in microsporidian spores are locked in a dimeric hibernating state.
Authors: Mathew McLaren / Rebecca Conners / Michail N Isupov / Patricia Gil-Díez / Lavinia Gambelli / Vicki A M Gold / Andreas Walter / Sean R Connell / Bryony Williams / Bertram Daum /
Abstract: Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be ...Translational control is an essential process for the cell to adapt to varying physiological or environmental conditions. To survive adverse conditions such as low nutrient levels, translation can be shut down almost entirely by inhibiting ribosomal function. Here we investigated eukaryotic hibernating ribosomes from the microsporidian parasite Spraguea lophii in situ by a combination of electron cryo-tomography and single-particle electron cryo-microscopy. We show that microsporidian spores contain hibernating ribosomes that are locked in a dimeric (100S) state, which is formed by a unique dimerization mechanism involving the beak region. The ribosomes within the dimer are fully assembled, suggesting that they are ready to be activated once the host cell is invaded. This study provides structural evidence for dimerization acting as a mechanism for ribosomal hibernation in microsporidia, and therefore demonstrates that eukaryotes utilize this mechanism in translational control.
History
DepositionMay 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Data processing / Refinement description / Category: em_3d_reconstruction / refine
Item: _em_3d_reconstruction.resolution / _refine.ls_d_res_high
Revision 1.2Sep 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_obsolete
Revision 1.3Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L50: RNA 28S
L70: RNA 5S
LA0: 60S ribosomal protein L8
LAA: uL15
LB0: 60S ribosomal protein L3
LC0: 60S ribosomal protein L4
LCC: 60S ribosomal protein L3
LD0: 60S ribosomal protein L5
LDD: 60S ribosomal protein L31
LE0: 60S ribosomal protein L6
LEE: 60S ribosomal protein L32
LF0: 60S ribosomal protein L7
LFF: 60S ribosomal protein L35a
LG0: 60S ribosomal protein L8
LGG: Ribosomal protein L34
LH0: 60S ribosomal protein L9
LHH: Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein
LI0: S60 ribosomal protein L10
LII: 60S ribosomal protein L36
LJ0: 60S ribosomal protein L11
LJJ: eL37
LL0: 60S ribosomal protein L13
LLL: 60S ribosomal protein L39
LM0: Transposase
LMM: Ubiquitin
LN0: Ribosomal protein L15
LO0: Ribosomal protein L13A
LOO: 60S ribosomal protein L44
LP0: 60S ribosomal protein L17
LPP: 60S ribosomal protein L37a
LQ0: 60S ribosomal protein L18
LR0: 60S ribosomal protein L19
LS0: 60S ribosomal protein L20
LT0: 60s ribosomal protein L21
LU0: 60S ribosomal protein L22
LV0: Ribosomal protein L23
LW0: Ribosomal protein L24E
LX0: 60S ribosomal protein L23a
LY0: 60S ribosomal protein L26
LZ0: 60S ribosomal protein L27
MD1: DNL-type domain-containing protein
S60: RNA 16S
SA0: 40S ribosomal protein S0
SAA: 40S ribosomal protein S26
SB0: eS1
SBB: eS27
SC0: 40S ribosomal protein S2
SCC: eS28
SD0: 40S ribosomal protein S3
SDD: 40S ribosomal protein S29
SE0: 40S ribosomal protein S4
SEE: eS30
SF0: 40S ribosomal protein S5
SFF: Ubiquitin/40s ribosomal protein S27a fusion
SG0: 40S ribosomal protein S6
SGG: Guanine nucleotide binding protein beta subunit
SH0: 40S ribosomal protein S7
SI0: 40S ribosomal protein S8
SJ0: 40S ribosomal protein S9
SK0: 40S ribosomal protein S10
SL0: 40S ribosomal protein S11
SM0: 40S ribosomal protein S12
SN0: 40S ribosomal protein S13
SO0: 40S ribosomal protein S14
SP0: Ribosomal protein S19
SQ0: 40S ribosomal protein S16
SR0: eS17
SS0: 40S ribosomal protein S18
ST0: 40S Ribosomal protein S19
SU0: 40S ribosomal protein S20
SV0: Ribosomal protein S21E
SW0: 40S ribosomal protein S15A
SX0: uS12
SY0: 40s ribosomal protein s24
SZ0: 40S ribosomal protein S25
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,647,09984
Polymers2,646,51075
Non-polymers5899
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules L50L70S60

#1: RNA chain RNA 28S


Mass: 849039.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#2: RNA chain RNA 5S


Mass: 38356.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#42: RNA chain RNA 16S


Mass: 444812.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)

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60S ribosomal protein ... , 27 types, 27 molecules LA0LB0LC0LCCLD0LDDLE0LEELF0LFFLG0LH0LIILJ0LL0LLLLOOLP0LPPLQ0LR0LS0LT0LU0LX0LY0LZ0

#3: Protein 60S ribosomal protein L8


Mass: 27005.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W736
#5: Protein 60S ribosomal protein L3


Mass: 44320.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XFB1
#6: Protein 60S ribosomal protein L4


Mass: 37241.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WCM8
#7: Protein 60S ribosomal protein L3


Mass: 12484.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAY0
#8: Protein 60S ribosomal protein L5


Mass: 33892.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XIG7
#9: Protein 60S ribosomal protein L31


Mass: 12854.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XW48
#10: Protein 60S ribosomal protein L6


Mass: 20220.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W5S3
#11: Protein 60S ribosomal protein L32


Mass: 16075.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XKE0
#12: Protein 60S ribosomal protein L7


Mass: 27935.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W946
#13: Protein 60S ribosomal protein L35a


Mass: 12757.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W662
#14: Protein 60S ribosomal protein L8


Mass: 23604.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XU63
#16: Protein 60S ribosomal protein L9


Mass: 21538.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XRZ9
#19: Protein 60S ribosomal protein L36


Mass: 11350.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WED1
#20: Protein 60S ribosomal protein L11


Mass: 19484.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WB69
#22: Protein 60S ribosomal protein L13


Mass: 19513.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVM9
#23: Protein 60S ribosomal protein L39


Mass: 6227.581 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XTP1
#28: Protein 60S ribosomal protein L44


Mass: 11990.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XL20
#29: Protein 60S ribosomal protein L17


Mass: 19114.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WDR4
#30: Protein 60S ribosomal protein L37a


Mass: 10151.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W6N9
#31: Protein 60S ribosomal protein L18


Mass: 21378.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAI2
#32: Protein 60S ribosomal protein L19


Mass: 19549.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WBY9
#33: Protein 60S ribosomal protein L20


Mass: 20043.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAG4
#34: Protein 60s ribosomal protein L21


Mass: 18344.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8F6
#35: Protein 60S ribosomal protein L22


Mass: 12854.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W958
#38: Protein 60S ribosomal protein L23a


Mass: 12557.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XFW8
#39: Protein 60S ribosomal protein L26


Mass: 15026.874 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W884
#40: Protein 60S ribosomal protein L27


Mass: 18247.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XU08

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Protein , 15 types, 15 molecules LAALHHLI0LJJLM0LMMMD1SB0SBBSCCSEESFFSGGSR0SX0

#4: Protein uL15


Mass: 16609.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#17: Protein Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein (Fragment),Ribosomal L29 protein


Mass: 14183.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7Y2
#18: Protein S60 ribosomal protein L10


Mass: 25142.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WBF8
#21: Protein eL37


Mass: 10517.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#24: Protein Transposase


Mass: 13258.343 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVN9
#25: Protein Ubiquitin


Mass: 14563.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XSQ3
#41: Protein DNL-type domain-containing protein


Mass: 17595.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W5K5
#45: Protein eS1


Mass: 25934.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#46: Protein eS27


Mass: 9189.923 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#48: Protein eS28


Mass: 7288.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#52: Protein eS30


Mass: 6816.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#54: Protein Ubiquitin/40s ribosomal protein S27a fusion


Mass: 16937.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W9X5
#56: Protein Guanine nucleotide binding protein beta subunit


Mass: 36182.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVG3
#67: Protein eS17


Mass: 14055.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#73: Protein uS12


Mass: 15822.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)

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Ribosomal protein ... , 7 types, 7 molecules LGGLN0LO0LV0LW0SP0SV0

#15: Protein Ribosomal protein L34


Mass: 12020.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7C6
#26: Protein Ribosomal protein L15


Mass: 24200.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7A2
#27: Protein Ribosomal protein L13A


Mass: 22885.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XUD8
#36: Protein Ribosomal protein L23


Mass: 15239.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XLC4
#37: Protein Ribosomal protein L24E


Mass: 15342.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XSY2
#65: Protein Ribosomal protein S19


Mass: 18514.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XKY9
#71: Protein Ribosomal protein S21E


Mass: 7768.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAC1

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40S ribosomal protein ... , 23 types, 23 molecules SA0SAASC0SD0SDDSE0SF0SG0SH0SI0SJ0SK0SL0SM0SN0SO0SQ0SS0ST0SU0SW0SY0SZ0

#43: Protein 40S ribosomal protein S0


Mass: 26201.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8R1
#44: Protein 40S ribosomal protein S26


Mass: 11974.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W9M7
#47: Protein 40S ribosomal protein S2


Mass: 27241.541 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7R5
#49: Protein 40S ribosomal protein S3


Mass: 27516.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAW0
#50: Protein 40S ribosomal protein S29


Mass: 7891.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XJB1
#51: Protein 40S ribosomal protein S4


Mass: 31442.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XG51
#53: Protein 40S ribosomal protein S5


Mass: 21982.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W4M9
#55: Protein 40S ribosomal protein S6


Mass: 26194.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WDE5
#57: Protein 40S ribosomal protein S7


Mass: 19132.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XV29
#58: Protein 40S ribosomal protein S8


Mass: 19912.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XGW2
#59: Protein 40S ribosomal protein S9


Mass: 21365.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8E3
#60: Protein 40S ribosomal protein S10


Mass: 12702.538 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XU48
#61: Protein 40S ribosomal protein S11


Mass: 18109.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8R0
#62: Protein 40S ribosomal protein S12


Mass: 14343.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7D2
#63: Protein 40S ribosomal protein S13


Mass: 16191.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVZ9
#64: Protein 40S ribosomal protein S14


Mass: 14708.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W6I0
#66: Protein 40S ribosomal protein S16


Mass: 16415.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WDU9
#68: Protein 40S ribosomal protein S18


Mass: 18171.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XJA1
#69: Protein 40S Ribosomal protein S19


Mass: 16603.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7P5
#70: Protein 40S ribosomal protein S20


Mass: 13777.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W986
#72: Protein 40S ribosomal protein S15A


Mass: 14620.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XK92
#74: Protein 40s ribosomal protein s24


Mass: 17189.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8J5
#75: Protein 40S ribosomal protein S25


Mass: 14777.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAV8

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Non-polymers , 1 types, 9 molecules

#76: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Ribosome / Type: RIBOSOME / Entity ID: #1-#64, #66-#75, #65 / Source: NATURAL
Source (natural)Organism: Spraguea lophii 42_110 (fungus)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 20 mA, Carbon coated grid / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288.15 K / Details: blot force -1 and blot time 4 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: 6000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Avg electron dose per subtomogram (e/Å2)Detector modeFilm or detector model
111.98120COUNTINGGATAN K2 SUMMIT (4k x 4k)
211.98120GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1IMOD4.12.10volume selection
2Warp1.1.0volume selection
3SerialEMimage acquisition
5Warp1.1.0CTF correction
12RELION3.1final Euler assignment
14RELION3.13D reconstruction
15Warp1.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 10.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1344 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 20 / Num. of volumes extracted: 6505
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementHighest resolution: 10.8 Å

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