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- PDB-8p60: Spraguea lophii ribosome dimer -

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Basic information

Entry
Database: PDB / ID: 8p60
TitleSpraguea lophii ribosome dimer
Components
  • (40S ribosomal protein ...) x 28
  • (60S ribosomal protein ...) x 28
  • (Ribosomal protein ...) x 9
  • DNL-type domain-containing protein
  • Guanine nucleotide binding protein beta subunit
  • RNA 16S
  • RNA 28S
  • RNA 5S
  • Ribosomal L29 protein
  • S60 ribosomal protein L10
  • Transposase
  • Ubiquitin
  • Ubiquitin/40s ribosomal protein S27a fusion
KeywordsRIBOSOME / Microsporidia
Function / homology
Function and homology information


preribosome / nonfunctional rRNA decay / preribosome, small subunit precursor / translational elongation / translational termination / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...preribosome / nonfunctional rRNA decay / preribosome, small subunit precursor / translational elongation / translational termination / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / maintenance of translational fidelity / protein tag activity / rRNA processing / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / 5S rRNA binding / ribosomal large subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / : / Ribosomal protein L32e, archaeal / : / : / : / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily ...CXXC motif containing zinc binding protein, eukaryotic / CXXC motif containing zinc binding protein, eukaryotic / : / Ribosomal protein L32e, archaeal / : / : / : / : / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e / Ribosomal protein L13e / S27a-like superfamily / Ribosomal protein L13e / 40S Ribosomal protein S10 / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal L40e family / Ribosomal protein S25 / S25 ribosomal protein / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein S27a / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / 60S ribosomal protein L6E / Ribosomal protein L7A/L8 / Ribosomal protein L13, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein L30/YlxQ / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L35A / 40S ribosomal protein S11, N-terminal / Ribosomal protein L35Ae / Ribosomal_S17 N-terminal / Ribosomal protein L35A superfamily / : / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e
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 / Small ribosomal subunit protein uS11 / Ribosomal protein L15 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / 40S ribosomal protein S5 / Uncharacterized protein / 60S ribosomal protein L6 / 60S ribosomal protein L35a / Small ribosomal subunit protein uS11 / Ribosomal protein L15 / Ribosomal protein L34 / 40S ribosomal protein S12 / 40S Ribosomal protein S19 / Small ribosomal subunit protein uS5 / 60S ribosomal protein L26 / 40S ribosomal protein S9 / 60s ribosomal protein L21 / 40s ribosomal protein s24 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS2 / 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 / Large ribosomal subunit protein uL4 / 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 / Large ribosomal subunit protein eL32 / 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: 14.3 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 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Data processing / Database references / Refinement description
Category: em_3d_reconstruction / pdbx_database_related / 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
SupersessionNov 13, 2024ID: 7QJH
Revision 1.4Nov 13, 2024Group: Advisory / Data collection / Structure summary
Category: em_admin / pdbx_database_PDB_obs_spr / pdbx_entry_details
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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: Ribosomal protein L18e/L15P
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
LI0: S60 ribosomal protein L10
LII: 60S ribosomal protein L36
LJ0: 60S ribosomal protein L11
LJJ: 60S ribosomal protein L37
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: 40S ribosomal protein S1
SBB: 40S ribosomal protein S27
SC0: 40S ribosomal protein S2
SCC: 40S ribosomal protein S28
SD0: 40S ribosomal protein S3
SDD: 40S ribosomal protein S29
SE0: 40S ribosomal protein S4
SEE: 40S ribosomal protein S30
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
SQ0: 40S ribosomal protein S16
SR0: 40S ribosomal protein S17
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: Ribosomal protein S12/S23
SY0: 40s ribosomal protein s24
SZ0: 40S ribosomal protein S25
K50: RNA 28S
K70: RNA 5S
KA0: 60S ribosomal protein L8
KAA: Ribosomal protein L18e/L15P
KB0: 60S ribosomal protein L3
KC0: 60S ribosomal protein L4
KCC: 60S ribosomal protein L3
KD0: 60S ribosomal protein L5
KDD: 60S ribosomal protein L31
KE0: 60S ribosomal protein L6
KEE: 60S ribosomal protein L32
KF0: 60S ribosomal protein L7
KFF: 60S ribosomal protein L35a
KG0: 60S ribosomal protein L8
KGG: Ribosomal protein L34
KH0: 60S ribosomal protein L9
KHH: Ribosomal L29 protein
KI0: S60 ribosomal protein L10
KII: 60S ribosomal protein L36
KJ0: 60S ribosomal protein L11
KJJ: 60S ribosomal protein L37
KL0: 60S ribosomal protein L13
KLL: 60S ribosomal protein L39
KM0: Transposase
KMM: Ubiquitin
KN0: Ribosomal protein L15
KO0: Ribosomal protein L13A
KOO: 60S ribosomal protein L44
KP0: 60S ribosomal protein L17
KPP: 60S ribosomal protein L37a
KQ0: 60S ribosomal protein L18
KR0: 60S ribosomal protein L19
KS0: 60S ribosomal protein L20
KT0: 60s ribosomal protein L21
KU0: 60S ribosomal protein L22
KV0: Ribosomal protein L23
KW0: Ribosomal protein L24E
KX0: 60S ribosomal protein L23a
KY0: 60S ribosomal protein L26
KZ0: 60S ribosomal protein L27
MD2: DNL-type domain-containing protein
R60: RNA 16S
RA0: 40S ribosomal protein S0
RAA: 40S ribosomal protein S26
RB0: 40S ribosomal protein S1
RBB: 40S ribosomal protein S27
RC0: 40S ribosomal protein S2
RCC: 40S ribosomal protein S28
RD0: 40S ribosomal protein S3
RDD: 40S ribosomal protein S29
RE0: 40S ribosomal protein S4
REE: 40S ribosomal protein S30
RF0: 40S ribosomal protein S5
RFF: Ubiquitin/40s ribosomal protein S27a fusion
RG0: 40S ribosomal protein S6
RGG: Guanine nucleotide binding protein beta subunit
RH0: 40S ribosomal protein S7
RI0: 40S ribosomal protein S8
RJ0: 40S ribosomal protein S9
RK0: 40S ribosomal protein S10
RL0: 40S ribosomal protein S11
RM0: 40S ribosomal protein S12
RN0: 40S ribosomal protein S13
RO0: 40S ribosomal protein S14
RQ0: 40S ribosomal protein S16
RR0: 40S ribosomal protein S17
RS0: 40S ribosomal protein S18
RT0: 40S Ribosomal protein S19
RU0: 40S ribosomal protein S20
RV0: Ribosomal protein S21E
RW0: 40S ribosomal protein S15A
RX0: Ribosomal protein S12/S23
RY0: 40s ribosomal protein s24
RZ0: 40S ribosomal protein S25
SP0: Ribosomal protein S19
RP0: Ribosomal protein S19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,294,197168
Polymers5,293,020150
Non-polymers1,17718
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 6 molecules L50K50L70K70S60R60

#1: RNA chain RNA 28S


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


Mass: 38356.801 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)

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60S ribosomal protein ... , 28 types, 56 molecules LA0KA0LB0KB0LC0KC0LCCKCCLD0KD0LDDKDDLE0KE0LEEKEELF0KF0LFFKFFLG0KG0LH0KH0LIIKIILJ0KJ0LJJKJJ...

#3: Protein 60S ribosomal protein L8


Mass: 27005.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#5: Protein 60S ribosomal protein L3


Mass: 44320.641 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WB69
#21: Protein 60S ribosomal protein L37 / eL37


Mass: 10517.657 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#22: Protein 60S ribosomal protein L13


Mass: 19513.141 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#31: Protein 60S ribosomal protein L18


Mass: 21378.133 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XU08

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Ribosomal protein ... , 9 types, 18 molecules LAAKAALGGKGGLN0KN0LO0KO0LV0KV0LW0KW0SV0RV0SX0RX0SP0RP0

#4: Protein Ribosomal protein L18e/L15P / uL15


Mass: 16609.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#15: Protein Ribosomal protein L34


Mass: 12020.348 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XSY2
#70: Protein Ribosomal protein S21E


Mass: 7768.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WAC1
#72: Protein Ribosomal protein S12/S23 / uS12


Mass: 15822.722 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#75: Protein Ribosomal protein S19


Mass: 18514.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XKY9

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Protein , 7 types, 14 molecules LHHKHHLI0KI0LM0KM0LMMKMMMD1MD2SFFRFFSGGRGG

#17: Protein Ribosomal L29 protein


Mass: 14183.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#18: Protein S60 ribosomal protein L10


Mass: 25142.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WBF8
#24: Protein Transposase


Mass: 13258.343 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: MYFIKPGCLIKKKFSIYTSIVISVIDNNSVVIQSYDKSDNGDVISIDREVINVSKIVPIGNIDIKNKSKKEIDGILVEENRNLKNKDDVLLMNDFERFKEQLKKEVEDMVIEEMA
Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVN9
#25: Protein Ubiquitin


Mass: 14563.868 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W5K5
#54: Protein Ubiquitin/40s ribosomal protein S27a fusion


Mass: 16937.791 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XVG3

+
40S ribosomal protein ... , 28 types, 56 molecules SA0RA0SAARAASB0RB0SBBRBBSC0RC0SCCRCCSD0RD0SDDRDDSE0RE0SEEREESF0RF0SG0RG0SH0RH0SI0RI0SJ0RJ0...

#43: Protein 40S ribosomal protein S0


Mass: 26201.186 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W9M7
#45: Protein 40S ribosomal protein S1 / eS1


Mass: 25934.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#46: Protein 40S ribosomal protein S27 / eS27


Mass: 9189.923 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#47: Protein 40S ribosomal protein S2


Mass: 27241.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7R5
#48: Protein 40S ribosomal protein S28 / eS28


Mass: 7288.479 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#49: Protein 40S ribosomal protein S3


Mass: 27516.459 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XG51
#52: Protein 40S ribosomal protein S30 / eS30


Mass: 6816.010 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#53: Protein 40S ribosomal protein S5


Mass: 21982.785 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#57: Protein 40S ribosomal protein S7


Mass: 19132.023 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W6I0
#65: Protein 40S ribosomal protein S16


Mass: 16415.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7WDU9
#66: Protein 40S ribosomal protein S17 / eS17


Mass: 14055.251 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus)
#67: Protein 40S ribosomal protein S18


Mass: 18171.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XJA1
#68: Protein 40S Ribosomal protein S19


Mass: 16603.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W7P5
#69: Protein 40S ribosomal protein S20


Mass: 13777.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W986
#71: Protein 40S ribosomal protein S15A


Mass: 14620.056 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7XK92
#73: Protein 40s ribosomal protein s24


Mass: 17189.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Spraguea lophii 42_110 (fungus) / References: UniProt: S7W8J5
#74: Protein 40S ribosomal protein S25


Mass: 14777.071 Da / Num. of mol.: 2 / 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, 18 molecules

#76: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

-
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-#75 / 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
8Cootmodel fitting
9UCSF ChimeraXmodel fitting
11REFMACmodel refinement
13RELION3.1final Euler assignment
15RELION3.13D reconstruction
16Warp1.1.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 14.3 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: RECIPROCAL
RefinementHighest resolution: 14.3 Å

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