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- PDB-4v6w: Structure of the D. melanogaster 80S ribosome -

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Basic information

Entry
Database: PDB / ID: 4v6w
TitleStructure of the D. melanogaster 80S ribosome
Components
  • (40S ribosomal protein ...) x 32
  • (60S ribosomal protein ...) x 44
  • 18S ribosomal RNA
  • 28S ribosomal RNA
  • 2S ribosomal RNA
  • 5.8S ribosomal RNA
  • 5S ribosomal RNA
  • 60S acidic ribosomal protein P0
  • E-tRNA
  • Elongation factor 2EEF2
  • Guanine nucleotide-binding protein subunit beta-like protein
  • Vig2, isoform B
KeywordsRIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry
Function / homology
Function and homology information


Peptide chain elongation / Synthesis of diphthamide-EEF2 / : / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / TCF dependent signaling in response to WNT / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / : / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / TCF dependent signaling in response to WNT / 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 / Senescence-Associated Secretory Phenotype (SASP) / Regulation of PLK1 Activity at G2/M Transition / Regulation of innate immune responses to cytosolic DNA / RMTs methylate histone arginines / Regulation of TNFR1 signaling / Metalloprotease DUBs / 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 / polytene chromosome chromocenter / 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 / Peroxisomal protein import / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Activation of NF-kappaB in B cells / 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 / Downstream TCR signaling / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / FCERI mediated NF-kB activation / Degradation of AXIN / Degradation of DVL / PINK1-PRKN Mediated Mitophagy / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Josephin domain DUBs / 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 / KEAP1-NFE2L2 pathway / 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 / 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 / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Spry regulation of FGF signaling / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling
Similarity search - Function
: / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 40S ribosomal protein SA, C-terminal domain / 60S acidic ribosomal protein P0 / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal ...: / Hyaluronan / mRNA binding family / RNA binding protein HABP4/SERBP1 / Hyaluronan/mRNA-binding protein / Hyaluronan / mRNA binding family / 60s Acidic ribosomal protein / 40S ribosomal protein SA, C-terminal domain / 60S acidic ribosomal protein P0 / 40S ribosomal protein SA C-terminus / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / Ribosomal protein L30e / Ribosomal protein L28e / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / : / Ribosomal protein L41 / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / Ribosomal protein L41 / Ribosomal protein S12e / 50S ribosomal protein L10, insertion domain superfamily / : / EF-G domain III/V-like / Small (40S) ribosomal subunit Asc1/RACK1 / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S26e signature. / Ribosomal protein S17e, conserved site / : / Ribosomal protein S2, eukaryotic / Tr-type G domain, conserved site / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein L29e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e signature. / Ribosomal L29e protein family / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / 40S ribosomal protein S11, N-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / 40S ribosomal protein S4, C-terminal domain / Ribosomal protein L34e, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal L22e protein family / Ribosomal protein L23/L25, N-terminal / 40S Ribosomal protein S10
Similarity search - Domain/homology
: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11A / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL3 ...: / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11A / 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 uL10 / Large ribosomal subunit protein uL4 / Small ribosomal subunit protein eS26 / Eukaryotic translation elongation factor 2 / 40S ribosomal protein S14b / 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 / Large ribosomal subunit protein eL22 / 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 / 40S ribosomal protein S15 / 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 / 40S ribosomal protein S10a / 60S ribosomal protein L34 / 60S ribosomal protein L27 / 40S ribosomal protein S27 / Vig2, isoform B / 40S ribosomal protein S30 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein eL24 / IP17351p / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL28 / FI01658p / 60S ribosomal protein L12 / 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: 6 Å
AuthorsAnger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R.
CitationJournal: Nature / Year: 2013
Title: Structures of the human and Drosophila 80S ribosome.
Authors: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann /
Abstract: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3J38, 3J3C, 3J39, 3J3E
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Apr 8, 2015Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details
Revision 1.5Feb 1, 2023Group: Database references
Category: citation_author / database_2 / pdbx_database_related
Item: _citation_author.name / _database_2.pdbx_DOI ..._citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

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Structure visualization

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Assembly

Deposited unit
Az: Elongation factor 2
Ag: Guanine nucleotide-binding protein subunit beta-like protein
AU: 40S ribosomal protein S20
AK: 40S ribosomal protein S10a
AO: 40S ribosomal protein S14
AX: 40S ribosomal protein S23
AM: 40S ribosomal protein S12
AS: 40S ribosomal protein S18
Ad: 40S ribosomal protein S29
AN: 40S ribosomal protein S13
AL: 40S ribosomal protein S11
AR: 40S ribosomal protein S17
AP: 40S ribosomal protein S15, isoform A
AT: 40S ribosomal protein S19a
AB: 40S ribosomal protein S3a
AA: 40S ribosomal protein SA
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
Ac: 40S ribosomal protein S28
AD: 40S ribosomal protein S3
Ae: 40S ribosomal protein S30, isoform A
Af: 40S ribosomal protein S27a
AJ: 40S ribosomal protein S9
AE: 40S ribosomal protein S4
AC: 40S ribosomal protein S2
AG: 40S ribosomal protein S6
AF: 40S ribosomal protein S5a
AH: 40S ribosomal protein S7
AW: 40S ribosomal protein S15Aa
AI: 40S ribosomal protein S8
AQ: 40S ribosomal protein S16
Ah: Vig2, isoform B
B2: 18S ribosomal RNA
BC: E-tRNA
Cz: 60S ribosomal protein L10a-2
Cq: 60S acidic ribosomal protein P0
CK: 60S ribosomal protein L12
CO: 60S ribosomal protein L13a
CL: 60S ribosomal protein L13
CV: 60S ribosomal protein L23
CM: 60S ribosomal protein L14
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
CA: 60S ribosomal protein L8
CS: 60S ribosomal protein L18a
CT: 60S ribosomal protein L21
CP: 60S ribosomal protein L17
CU: 60S ribosomal protein L22
CX: 60S ribosomal protein L23A
CY: 60S ribosomal protein L26
CW: 60S ribosomal protein L24
CZ: 60S ribosomal protein L27
Cr: 60S ribosomal protein L28
Ch: 60S ribosomal protein L35
Cb: 60S ribosomal protein L29
CB: 60S ribosomal protein L3
CF: 60S ribosomal protein L7
Cc: 60S ribosomal protein L30
Cd: 60S ribosomal protein L31
Ce: 60S ribosomal protein L32
Cf: 60S ribosomal protein L35A
Cg: 60S ribosomal protein L34a
Ci: 60S ribosomal protein L36
Cj: 60S ribosomal protein L37-A
Ck: 60S ribosomal protein L38
Cl: 60S ribosomal protein L39
CC: 60S ribosomal protein L4
Cm: 60S ribosomal protein L40
Cn: 60S ribosomal protein L41
Cp: 60S ribosomal protein L37a
Co: 60S ribosomal protein L36A
CJ: 60S ribosomal protein L11
CH: 60S ribosomal protein L9
CE: 60S ribosomal protein L6, isoform A
CG: 60S ribosomal protein L7a
A5: 28S ribosomal RNA
A9: 2S ribosomal RNA
A7: 5S ribosomal RNA
A8: 5.8S ribosomal RNA


Theoretical massNumber of molelcules
Total (without water)3,670,25086
Polymers3,670,25086
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules AzAgAhCq

#1: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 94585.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P13060
#2: 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
#35: Protein Vig2, isoform B


Mass: 13542.481 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VBX3
#39: Protein 60S acidic ribosomal protein P0 / / 60S ribosomal protein L10E


Mass: 24401.459 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P05388*PLUS

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40S ribosomal protein ... , 32 types, 32 molecules AUAKAOAXAMASAdANALARAPATABAAAVAYAZAaAbAcADAeAfAJAEACAGAFAHAWAIAQ

#3: Protein 40S ribosomal protein S20 /


Mass: 13513.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55828
#4: Protein 40S ribosomal protein S10a / Ribosome


Mass: 18259.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VB14
#5: Protein 40S ribosomal protein S14 /


Mass: 16294.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P14130, UniProt: C0HKA0*PLUS
#6: 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
#7: Protein 40S ribosomal protein S12 /


Mass: 15191.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P80455
#8: Protein 40S ribosomal protein S18 /


Mass: 17649.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41094
#9: Protein 40S ribosomal protein S29 /


Mass: 6603.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VH69
#10: Protein 40S ribosomal protein S13 /


Mass: 17216.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q03334
#11: 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
#12: Protein 40S ribosomal protein S17 /


Mass: 15313.757 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P17704
#13: Protein 40S ribosomal protein S15, isoform A / Ribosome / RE08270p


Mass: 17073.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q7JZW2
#14: Protein 40S ribosomal protein S19a / Ribosome


Mass: 17327.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P39018
#15: Protein 40S ribosomal protein S3a / / C3 protein


Mass: 30393.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55830
#16: Protein 40S ribosomal protein SA / / K14 / Laminin receptor homolog / Protein stubarista


Mass: 35384.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P38979
#17: Protein 40S ribosomal protein S21 / / Overgrown hematopoietic organs at 23B


Mass: 9031.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O76927
#18: Protein 40S ribosomal protein S24 /


Mass: 15082.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W229
#19: Protein 40S ribosomal protein S25 /


Mass: 13234.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48588
#20: Protein 40S ribosomal protein S26 / / DS31


Mass: 13300.712 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P13008
#21: 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
#22: Protein 40S ribosomal protein S28 /


Mass: 7489.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W334
#23: Protein 40S ribosomal protein S3 /


Mass: 27515.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q06559
#24: Protein 40S ribosomal protein S30, isoform A / Ribosome / Ribosomal protein S30 / isoform B


Mass: 14608.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VDH8
#25: Protein 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
#26: Protein 40S ribosomal protein S9 /


Mass: 22672.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55935
#27: 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
#28: Protein 40S ribosomal protein S2 / / Protein strings of pearls


Mass: 28947.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P31009
#29: Protein 40S ribosomal protein S6 /


Mass: 28478.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P29327
#30: Protein 40S ribosomal protein S5a / Ribosome


Mass: 25471.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24186
#31: 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
#32: Protein 40S ribosomal protein S15Aa / Ribosome


Mass: 14796.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48149
#33: Protein 40S ribosomal protein S8 /


Mass: 23814.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q8MLY8
#34: 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

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RNA chain , 6 types, 6 molecules B2BCA5A9A7A8

#36: 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: M21017
#37: RNA chain E-tRNA


Mass: 24249.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: K00325
#83: RNA chain 28S ribosomal RNA /


Mass: 1277668.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: GenBank: M21017
#84: 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: M21017
#85: 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: M25016
#86: 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: M21017

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60S ribosomal protein ... , 44 types, 44 molecules CzCKCOCLCVCMCaCNCICDCQCRCACSCTCPCUCXCYCWCZCrChCbCBCFCcCdCeCf...

#38: Protein 60S ribosomal protein L10a-2 / Ribosome


Mass: 24404.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VTP4
#40: Protein 60S ribosomal protein L12 /


Mass: 17701.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W1B9
#41: 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
#42: Protein 60S ribosomal protein L13 / / BBC1 protein homolog


Mass: 25012.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41126
#43: Protein 60S ribosomal protein L23 / / L17A


Mass: 14962.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P48159
#44: Protein 60S ribosomal protein L14 /


Mass: 19217.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P55841
#45: 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
#46: Protein 60S ribosomal protein L15 /


Mass: 24388.592 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O17445
#47: Protein 60S ribosomal protein L10 / / QM protein homolog / dQM


Mass: 25579.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O61231
#48: Protein 60S ribosomal protein L5 /


Mass: 34101.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W5R8
#49: Protein 60S ribosomal protein L18 /


Mass: 21713.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VS34
#50: 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
#51: Protein 60S ribosomal protein L8 /


Mass: 27957.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V3G1
#52: Protein 60S ribosomal protein L18a /


Mass: 21076.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P41093
#53: Protein 60S ribosomal protein L21 / / RH06526p / RE62581p


Mass: 18519.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V9M7
#54: Protein 60S ribosomal protein L17 /


Mass: 21642.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W3W8
#55: Protein 60S ribosomal protein L22 /


Mass: 30675.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P50887
#56: Protein 60S ribosomal protein L23A / / FI01658p


Mass: 29539.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W0A8
#57: Protein 60S ribosomal protein L26 / / RE17611p


Mass: 17322.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VVU2
#58: Protein 60S ribosomal protein L24 /


Mass: 17568.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJY6
#59: Protein 60S ribosomal protein L27 /


Mass: 15945.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VBN5
#60: Protein 60S ribosomal protein L28 /


Mass: 16067.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VZS5
#61: Protein 60S ribosomal protein L35 / / FI02809p


Mass: 14491.677 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W499
#62: Protein 60S ribosomal protein L29 / / L43


Mass: 8945.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q24154
#63: Protein 60S ribosomal protein L3 /


Mass: 47020.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O16797
#64: Protein 60S ribosomal protein L7 /


Mass: 29615.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P32100
#65: Protein 60S ribosomal protein L30 / / RE25263p


Mass: 12253.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VJ19
#66: Protein 60S ribosomal protein L31 /


Mass: 14563.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V597
#67: Protein 60S ribosomal protein L32 / / Ribosomal protein 49


Mass: 16060.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P04359
#68: Protein 60S ribosomal protein L35A / / RH44960p / RE17737p


Mass: 17701.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VNB9
#69: Protein 60S ribosomal protein L34a / Ribosome / FI02850p


Mass: 18117.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VBH8
#70: Protein 60S ribosomal protein L36 / / Protein minute(1)1B


Mass: 13541.192 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P49630
#71: Protein 60S ribosomal protein L37-A / Ribosome


Mass: 10673.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VXX8
#72: 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
#73: Protein 60S ribosomal protein L39 / / Ribosomal protein 46


Mass: 6318.640 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: O16130
#74: Protein 60S ribosomal protein L4 / / L1


Mass: 45120.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P09180
#75: Protein 60S ribosomal protein L40 /


Mass: 6200.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P18101
#76: Protein/peptide 60S ribosomal protein L41 / / RE63504p


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


Mass: 10335.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VMU4
#78: Protein 60S ribosomal protein L36A / / IP17351p


Mass: 12540.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9VLT7
#79: Protein 60S ribosomal protein L11 /


Mass: 21153.545 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P46222
#80: 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
#81: Protein 60S ribosomal protein L6, isoform A / Ribosome


Mass: 27766.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: Q9V9W2
#82: Protein 60S ribosomal protein L7a /


Mass: 30802.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: UniProt: P46223

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeParent-ID
280S D. melanogaster ribosomeRIBOSOME1
180S ribosome with E-tRNA, EF-2, and Vig2COMPLEX0
Molecular weightValue: 4 MDa / Experimental value: NO
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %
Details: Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Mar 10, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 90000 X / Calibrated magnification: 90000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: GATAN LIQUID NITROGEN
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: each subvolume
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Projection matching / Resolution: 6 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 134500 / Nominal pixel size: 1.2375 Å / Actual pixel size: 1.2375 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms46290 0 0 0 46290

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