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- PDB-6xu6: Drosophila melanogaster Testis 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 6xu6
TitleDrosophila melanogaster Testis 80S ribosome
Components
  • (40S ribosomal protein ...) x 30
  • (60S ribosomal protein ...) x 31
  • (Ribosomal protein ...) x 2
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 2S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • FI02809p
  • GEO07301p1
  • GEO07453p1
  • GEO07455p1
  • Guanine nucleotide-binding protein subunit beta-like protein
  • IP17216p
  • LP04564p
  • Probable 60S ribosomal protein L37-B
  • RE25263p
  • RE62581p
  • RH48056p
  • TA01007p
  • Ubiquitin-40S ribosomal protein S27a
  • Ubiquitin-60S ribosomal protein L40
KeywordsRIBOSOME / Specialised ribosome / Drosophila melanogaster / Testis
Function / homology
Function and homology information


APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol ...APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of TP53 Degradation / Cyclin D associated events in G1 / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / GTP hydrolysis and joining of the 60S ribosomal subunit / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Protein methylation / ER Quality Control Compartment (ERQC) / Iron uptake and transport / RAS processing / Pexophagy / Regulation of BACH1 activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Regulation of pyruvate metabolism / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translesion synthesis by POLK / Translesion synthesis by POLI / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Translesion Synthesis by POLH / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC-Cdc20 mediated degradation of Nek2A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / Degradation of AXIN / Degradation of DVL / Regulation of TNFR1 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Peroxisomal protein import / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Nuclear CI is degraded / ABC-family proteins mediated transport / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / PINK1-PRKN Mediated Mitophagy / Josephin domain DUBs / Dual Incision in GG-NER / Dual incision in TC-NER / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / KEAP1-NFE2L2 pathway / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Ubiquitination and proteolysis of phosphorylated CI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Interleukin-1 signaling / Regulation of signaling by CBL / pupariation / Downregulation of ERBB4 signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Protein hydroxylation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Deactivation of the beta-catenin transactivating complex / Hedgehog ligand biogenesis / Regulation of necroptotic cell death / EGFR downregulation
Similarity search - Function
Interferon-related developmental regulator, C-terminal / Interferon-related developmental regulator, N-terminal / Interferon-related developmental regulator / Interferon-related protein conserved region / Interferon-related developmental regulator (IFRD) / : / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain ...Interferon-related developmental regulator, C-terminal / Interferon-related developmental regulator, N-terminal / Interferon-related developmental regulator / Interferon-related protein conserved region / Interferon-related developmental regulator (IFRD) / : / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L18e / Ribosomal protein 60S L18 and 50S L18e / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / metallochaperone-like domain / TRASH domain / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L1 signature. / Ribosomal protein L1 / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S2, eukaryotic / Small (40S) ribosomal subunit Asc1/RACK1 / S27a-like superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein L27e, conserved site / Ribosomal protein L27e signature. / Ribosomal protein L44e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein L10e / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein L13e / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein L19, eukaryotic / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein S30 / : / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / : / Ribosomal protein L19/L19e conserved site / Ribosomal protein L19e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L34e, conserved site / Ribosomal protein L34e signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein L30e signature 1. / Ribosomal protein S3Ae signature. / Ribosomal_S19e / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a
Similarity search - Domain/homology
: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / IP17216p / Small ribosomal subunit protein uS11A ...: / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / IP17216p / Small ribosomal subunit protein uS11A / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL22 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL15 / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein eS21 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS26 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS17 / Ubiquitin-ribosomal protein eL40 fusion protein / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein eL19 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS4 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL20 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein eL13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein eS25 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL14 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein eL29 / Small ribosomal subunit protein uS7A / RH08962p / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS12 / 60S ribosomal protein L41 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL31 / 60S ribosomal protein L21 / Large ribosomal subunit protein eL6 / Small ribosomal subunit protein eS7 / 60S ribosomal protein L27 / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL13 / Interferon-related developmental regulator 1 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS10B / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein L37-2 / 40S ribosomal protein S24 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein uL22 / 60S ribosomal protein L35 / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL18
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHopes, T. / Agapiou, M. / Norris, K. / McCarthy, C.G.P. / OConnell, M.J. / Fontana, J. / Aspden, J.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007407/1 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Ribosome heterogeneity in Drosophila melanogaster gonads through paralog-switching.
Authors: Tayah Hopes / Karl Norris / Michaela Agapiou / Charley G P McCarthy / Philip A Lewis / Mary J O'Connell / Juan Fontana / Julie L Aspden /
Abstract: Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have ...Ribosomes have long been thought of as homogeneous macromolecular machines, but recent evidence suggests they are heterogeneous and could be specialised to regulate translation. Here, we have characterised ribosomal protein heterogeneity across 4 tissues of Drosophila melanogaster. We find that testes and ovaries contain the most heterogeneous ribosome populations, which occurs through a combination of paralog-enrichment and paralog-switching. We have solved structures of ribosomes purified from in vivo tissues by cryo-EM, revealing differences in precise ribosomal arrangement for testis and ovary 80S ribosomes. Differences in the amino acid composition of paralog pairs and their localisation on the ribosome exterior indicate paralog-switching could alter the ribosome surface, enabling different proteins to regulate translation. One testis-specific paralog-switching pair is also found in humans, suggesting this is a conserved site of ribosome heterogeneity. Overall, this work allows us to propose that mRNA translation might be regulated in the gonads through ribosome heterogeneity, providing a potential means of ribosome specialisation.
History
DepositionJan 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 21, 2022Group: Database references / Refinement description
Category: citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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_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

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Structure visualization

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Assembly

Deposited unit
AA: 40S ribosomal protein SA
CA: 60S ribosomal protein L8
AB: 40S ribosomal protein S3a
CB: 60S ribosomal protein L3
AC: 40S ribosomal protein S2
CC: 60S ribosomal protein L4
Ag: Guanine nucleotide-binding protein subunit beta-like protein
AU: 40S ribosomal protein S20
AX: 40S ribosomal protein S23
AM: 40S ribosomal protein S12
Ad: 40S ribosomal protein S29
AN: 40S ribosomal protein S13
AL: 40S ribosomal protein S11
AR: 40S ribosomal protein S17
AP: GEO07301p1
AV: 40S ribosomal protein S21
AY: 40S ribosomal protein S24
AZ: 40S ribosomal protein S25
Aa: 40S ribosomal protein S26
Ab: 40S ribosomal protein S27
AD: 40S ribosomal protein S3
Ae: 40S ribosomal protein S30
Af: Ubiquitin-40S ribosomal protein S27a
AJ: 40S ribosomal protein S9
Ca: 60S ribosomal protein L27a
CN: 60S ribosomal protein L15
CI: 60S ribosomal protein L10
CD: 60S ribosomal protein L5
CQ: 60S ribosomal protein L18
CR: 60S ribosomal protein L19
CS: 60S ribosomal protein L18a
CT: RE62581p
CP: 60S ribosomal protein L17
CX: IP17216p
CY: GEO07453p1
CZ: 60S ribosomal protein L27
Cr: 60S ribosomal protein L28
Ch: FI02809p
Cb: 60S ribosomal protein L29
Cc: RE25263p
Ce: 60S ribosomal protein L32
Cf: GEO07455p1
Ci: 60S ribosomal protein L36
Ck: 60S ribosomal protein L38
Cl: 60S ribosomal protein L39
Cm: Ubiquitin-60S ribosomal protein L40
Cn: 60S ribosomal protein L41
Cp: 60S ribosomal protein L37a
Co: TA01007p
CJ: 60S ribosomal protein L11
CH: 60S ribosomal protein L9
CE: Ribosomal protein L6, isoform A
CG: 60S ribosomal protein L7a
A9: 2S ribosomal RNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA
Cz: 60S ribosomal protein L10a-2
B2: 18S ribosomal RNA
A5: 28S ribosomal RNA
AE: 40S ribosomal protein S4
AG: 40S ribosomal protein S6
AH: 40S ribosomal protein S7
AI: 40S ribosomal protein S8
AQ: 40S ribosomal protein S16
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: 60S ribosomal protein L23
CM: 60S ribosomal protein L14
DA: LP04564p
AK: 40S ribosomal protein S10b
AT: 40S ribosomal protein S19a
AF: 40S ribosomal protein S5a
AO: 40S ribosomal protein S14a
Ac: 40S ribosomal protein S28
AW: 40S ribosomal protein S15Aa
CW: 60S ribosomal protein L24
Cg: RH48056p
CU: Ribosomal protein L22-like protein
Cj: Probable 60S ribosomal protein L37-B
CF: 60S ribosomal protein L7
Cd: 60S ribosomal protein L31
AS: 40S ribosomal protein S18


Theoretical massNumber of molelcules
Total (without water)3,399,51082
Polymers3,399,51082
Non-polymers00
Water00
1


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

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Components

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40S ribosomal protein ... , 30 types, 30 molecules AAABACAUAXAMAdANALARAVAYAZAaAbADAeAJAEAGAHAIAQAKATAFAOAcAWAS

#1: Protein 40S ribosomal protein SA / K14 / Laminin receptor homolog / Protein stubarista


Mass: 24651.229 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P38979
#3: Protein 40S ribosomal protein S3a / C3 protein


Mass: 25633.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55830
#5: Protein 40S ribosomal protein S2 / Protein strings of pearls


Mass: 24836.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P31009
#8: Protein 40S ribosomal protein S20


Mass: 11677.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55828
#9: Protein 40S ribosomal protein S23


Mass: 16054.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q8T3U2
#10: Protein 40S ribosomal protein S12


Mass: 13221.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P80455
#11: Protein 40S ribosomal protein S29


Mass: 6197.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VH69
#12: Protein 40S ribosomal protein S13


Mass: 17085.236 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q03334
#13: Protein 40S ribosomal protein S11


Mass: 18149.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q0E9B6
#14: Protein 40S ribosomal protein S17


Mass: 14012.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P17704
#16: Protein 40S ribosomal protein S21 / Overgrown hematopoietic organs at 23B


Mass: 8883.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O76927
#17: Protein 40S ribosomal protein S24


Mass: 14549.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W229
#18: Protein 40S ribosomal protein S25


Mass: 8640.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48588
#19: Protein 40S ribosomal protein S26 / DS31


Mass: 12412.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P13008
#20: Protein 40S ribosomal protein S27


Mass: 9382.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VBU9
#21: Protein 40S ribosomal protein S3


Mass: 25466.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q06559
#22: Protein 40S ribosomal protein S30


Mass: 6670.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JYY0
#24: Protein 40S ribosomal protein S9


Mass: 21326.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55935
#60: Protein 40S ribosomal protein S4


Mass: 29191.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41042
#61: Protein 40S ribosomal protein S6


Mass: 26639.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P29327
#62: Protein 40S ribosomal protein S7


Mass: 22209.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VA91
#63: Protein 40S ribosomal protein S8


Mass: 23683.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q8MLY8
#64: Protein 40S ribosomal protein S16


Mass: 16806.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W237
#70: Protein 40S ribosomal protein S10b


Mass: 10750.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VWG3
#71: Protein 40S ribosomal protein S19a


Mass: 16044.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P39018
#72: Protein 40S ribosomal protein S5a


Mass: 21297.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24186
#73: Protein 40S ribosomal protein S14a


Mass: 13615.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: C0HKA0
#74: Protein 40S ribosomal protein S28


Mass: 7114.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W334
#75: Protein 40S ribosomal protein S15Aa


Mass: 14665.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48149
#82: Protein 40S ribosomal protein S18


Mass: 15677.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41094

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60S ribosomal protein ... , 31 types, 31 molecules CACBCCCaCNCICDCQCRCSCPCZCrCbCeCiCkClCnCpCJCHCGCzCOCLCVCMCWCFCd

#2: Protein 60S ribosomal protein L8


Mass: 27584.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V3G1
#4: Protein 60S ribosomal protein L3


Mass: 46861.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O16797
#6: Protein 60S ribosomal protein L4 / L1


Mass: 44162.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P09180
#25: Protein 60S ribosomal protein L27a


Mass: 17070.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41092
#26: Protein 60S ribosomal protein L15


Mass: 24257.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O17445
#27: Protein 60S ribosomal protein L10 / QM protein homolog / dQM


Mass: 25448.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O61231
#28: Protein 60S ribosomal protein L5


Mass: 33138.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W5R8
#29: Protein 60S ribosomal protein L18


Mass: 21582.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VS34
#30: Protein 60S ribosomal protein L19


Mass: 24065.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P36241
#31: Protein 60S ribosomal protein L18a


Mass: 20588.100 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41093
#33: Protein 60S ribosomal protein L17


Mass: 21510.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W3W8
#36: Protein 60S ribosomal protein L27


Mass: 15813.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VBN5
#37: Protein 60S ribosomal protein L28


Mass: 14917.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VZS5
#39: Protein 60S ribosomal protein L29 / L43


Mass: 8814.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24154
#41: Protein 60S ribosomal protein L32 / Ribosomal protein 49


Mass: 15817.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P04359
#43: Protein 60S ribosomal protein L36 / Protein minute(1)1B


Mass: 13340.935 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P49630
#44: Protein 60S ribosomal protein L38


Mass: 8219.802 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W5N2
#45: Protein/peptide 60S ribosomal protein L39 / Ribosomal protein 46


Mass: 6187.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O16130
#47: Protein/peptide 60S ribosomal protein L41


Mass: 3416.400 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q962S2
#48: Protein 60S ribosomal protein L37a


Mass: 10204.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VMU4
#50: Protein 60S ribosomal protein L11


Mass: 20895.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P46222
#51: Protein 60S ribosomal protein L9


Mass: 21425.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P50882
#53: Protein 60S ribosomal protein L7a


Mass: 27518.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P46223
#57: Protein 60S ribosomal protein L10a-2


Mass: 24317.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VTP4
#65: Protein 60S ribosomal protein L13a


Mass: 23701.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VNE9
#66: Protein 60S ribosomal protein L13 / BBC1 protein homolog


Mass: 24081.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41126
#67: Protein 60S ribosomal protein L23 / L17A


Mass: 14243.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48159
#68: Protein 60S ribosomal protein L14


Mass: 18487.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55841
#76: Protein 60S ribosomal protein L24


Mass: 6900.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJY6
#80: Protein 60S ribosomal protein L7


Mass: 26465.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P32100
#81: Protein 60S ribosomal protein L31


Mass: 12798.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V597

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Protein , 14 types, 14 molecules AgAPAfCTCXCYChCcCfCmCoDACgCj

#7: Protein Guanine nucleotide-binding protein subunit beta-like protein / Receptor of activated protein kinase C homolog


Mass: 35661.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O18640
#15: Protein GEO07301p1 / RE08270p / Ribosomal protein S15 / isoform A


Mass: 14504.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JZW2
#23: Protein Ubiquitin-40S ribosomal protein S27a


Mass: 9421.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P15357
#32: Protein RE62581p / RH06526p / Ribosomal protein L21 / isoform A / isoform B / isoform C


Mass: 18388.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V9M7
#34: Protein IP17216p


Mass: 13981.525 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: A1A6X4
#35: Protein GEO07453p1 / RE17611p / Ribosomal protein L26 / isoform A / isoform B / isoform C


Mass: 15337.095 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VVU2
#38: Protein FI02809p / Ribosomal protein L35 / isoform A / isoform B / isoform C


Mass: 14491.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W499
#40: Protein RE25263p / Ribosomal protein L30 / isoform B / isoform C / isoform E


Mass: 11035.795 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJ19
#42: Protein GEO07455p1 / RE17737p / RH44960p / Ribosomal protein L35A


Mass: 17701.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VNB9
#46: Protein Ubiquitin-60S ribosomal protein L40 / CEP52


Mass: 6200.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P18101
#49: Protein TA01007p


Mass: 12540.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: C5WLN8
#69: Protein LP04564p


Mass: 41409.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VQI5
#77: Protein RH48056p / Ribosomal protein L34b / isoform A / isoform B / isoform C / isoform D


Mass: 12095.448 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VHE5
#79: Protein Probable 60S ribosomal protein L37-B


Mass: 9978.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W1U6

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Ribosomal protein ... , 2 types, 2 molecules CECU

#52: Protein Ribosomal protein L6, isoform A


Mass: 26179.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V9W2
#78: Protein Ribosomal protein L22-like protein


Mass: 11525.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: E2JE76

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RNA chain , 5 types, 5 molecules A9A7A8B2A5

#54: RNA chain 2S ribosomal RNA


Mass: 9665.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: NR_133545.1
#55: RNA chain 5S ribosomal RNA


Mass: 38627.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: 174298
#56: RNA chain 5.8S ribosomal RNA


Mass: 39616.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: 158246
#58: RNA chain 18S ribosomal RNA


Mass: 641830.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: 158246
#59: RNA chain 28S ribosomal RNA


Mass: 1278930.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: NR_133562.1

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Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Drosophila melanogaster testis 80S ribosome / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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
Image recordingElectron dose: 80 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46878 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4V6W

4v6w


Accession code: 4V6W / Source name: PDB / Type: experimental model

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