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- PDB-6p5j: Structure of a mammalian 80S ribosome in complex with the Israeli... -

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Basic information

Entry
Database: PDB / ID: 6p5j
TitleStructure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)
Components
  • 18S rRNA18S ribosomal RNA
  • 28S rRNA28S ribosomal RNA
  • 5.8S rRNA5.8S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • IAPV-IRES
  • L14e
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL23
  • eL24
  • eL27
  • eL28
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL35
  • eL36
  • eL37
  • eL38
  • eL39
  • eL40
  • eL41
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS29
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uL1
  • uL11
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL24
  • uL3
  • uL30
  • uL4
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Israeli Acute Paralysis Virus / Internal Ribosome Entry Site / IRES / Small Ribosomal Subunit / 40S / Large Ribosomal Subunit / 60S / 80S / ribosomes
Function / homology
Function and homology information


positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis ...positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / regulation of translation involved in cellular response to UV / negative regulation of DNA repair / oxidized pyrimidine DNA binding / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / response to TNF agonist / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / NF-kappaB complex / cytosolic ribosome / positive regulation of endodeoxyribonuclease activity / oxidized purine DNA binding / protein kinase A binding / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of T cell receptor signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / spindle assembly / positive regulation of JUN kinase activity / ribosomal small subunit biogenesis / polysome / positive regulation of microtubule polymerization / cellular response to leukemia inhibitory factor / Hsp70 protein binding / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / positive regulation of interleukin-2 production / rough endoplasmic reticulum / positive regulation of translation / mitotic spindle / ruffle membrane / Hsp90 protein binding / small ribosomal subunit rRNA binding / chromosome segregation / DNA damage response, detection of DNA damage / mRNA 5'-UTR binding / cellular response to gamma radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / rRNA processing / cellular response to hydrogen peroxide / positive regulation of NIK/NF-kappaB signaling / cytoplasmic translation / cytosolic large ribosomal subunit / large ribosomal subunit / 5S rRNA binding / cellular response to tumor necrosis factor / cytosolic small ribosomal subunit / small ribosomal subunit / mitochondrial inner membrane / microtubule binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / postsynaptic density / positive regulation of NF-kappaB transcription factor activity / mitochondrial matrix / cell differentiation / translation / cell division / synapse / mRNA binding / transcription factor binding / apoptotic process / protein-containing complex binding / nucleolus / protein kinase binding / Golgi apparatus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol
Ribosomal protein S27a / Ribosomal protein L4 domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19/S15, superfamily ...Ribosomal protein S27a / Ribosomal protein L4 domain superfamily / Ribosomal protein L15e core domain superfamily / Ribosomal protein S7 domain / Ribosomal protein L1-like / Ribosomal protein L1, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal protein L39e domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein S19/S15, superfamily / Ribosomal protein L24e, conserved site / 60S ribosomal protein L4, C-terminal domain / in:ipr023106: / Ribosomal protein S15P / Ribosomal protein L30e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein S4/S9 / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein L15e, conserved site / 40S ribosomal protein S4, C-terminal domain / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19, eukaryotic / 40S ribosomal protein S11, N-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein S10 domain / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal L28e/Mak16 / Ribosomal protein S28e conserved site / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L5, conserved site / Ribosomal protein S7, conserved site / Winged helix-like DNA-binding domain superfamily / Ribosomal S24e conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S11, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L30, conserved site / WD40-repeat-containing domain / Ribosomal protein L10e/L16 / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L19/L19e, domain 1 / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Ribosomal protein L35Ae, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S9, conserved site / Ubiquitin domain / Ribosomal protein S5 domain 2-type fold / G-protein beta WD-40 repeat / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L23 / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin conserved site / Ribosomal protein S13, conserved site / Ribosomal protein L3, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein L32e superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein L2, domain 2 / Ribosomal protein L34e / KH domain / Ribosomal protein S3, C-terminal domain / Ribosomal S3Ae family / Ribosomal L28e protein family / Ribosomal L37ae protein family / Ribosomal protein L44
60S ribosomal protein L35a / Uncharacterized protein / 60S ribosomal protein L29 / 40S ribosomal protein S12 / 60S ribosomal protein L21 / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L41 ...60S ribosomal protein L35a / Uncharacterized protein / 60S ribosomal protein L29 / 40S ribosomal protein S12 / 60S ribosomal protein L21 / Ribosomal_L23eN domain-containing protein / Ribosomal protein L24 / 40S ribosomal protein S9 / Ribosomal protein L10 / 60S ribosomal protein L41 / 60S ribosomal protein L14 / Ribosomal protein L37 / 60S ribosomal protein L34 / 60S ribosomal protein L35 / 60S ribosomal protein L4 / 40S ribosomal protein S26 / 60S ribosomal protein L30 / 40S ribosomal protein S25 / 40S ribosomal protein S30 / 60S ribosomal protein L23 / 40S ribosomal protein S24 / Ribosomal protein L15 / 40S ribosomal protein S23 / Ribosomal_L18_c domain-containing protein / Uncharacterized protein / 60S ribosomal protein L9 / 40S ribosomal protein S7 / 40S ribosomal protein S15a / Uncharacterized protein / 60S ribosomal protein L7a / 40S ribosomal protein S3a / Ribosomal protein L26 / 40S ribosomal protein S13 / 60S ribosomal protein L27a / Ribosomal protein / 60S ribosomal protein L6 / 40S ribosomal protein S27a / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S20 / Ribosomal protein S5 / 40S ribosomal protein S28 / 40S ribosomal protein S29 / 60S ribosomal protein L36 / 60S ribosomal protein L28 / Uncharacterized protein / Ribosomal protein L32 / Uncharacterized protein / 40S ribosomal protein S15 / 40S ribosomal protein S27 / 60S ribosomal protein L27 / 60S ribosomal protein L9 / 60S ribosomal protein L17 / 60S ribosomal protein L31 / 40S ribosomal protein S17 / Uncharacterized protein / Ribosomal protein L19 / 60S ribosomal protein L8 / Uncharacterized protein / 40S ribosomal protein S11 / S10_plectin domain-containing protein / 40S ribosomal protein S18 / 40S ribosomal protein S3 / 40S ribosomal protein S19 / 40S ribosomal protein S21 / 40S ribosomal protein S6 / Ribosomal protein L3 / 40S ribosomal protein S4 / 60S ribosomal protein L11
Biological speciesIsraeli acute paralysis virus
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsAcosta-Reyes, F.J. / Neupane, R. / Frank, J. / Fernandez, I.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM029169 United States
CitationJournal: EMBO J / Year: 2019
Title: The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
Authors: Francisco Acosta-Reyes / Ritam Neupane / Joachim Frank / Israel S Fernández /
Abstract: Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a ...Colony collapse disorder (CCD) is a multi-faceted syndrome decimating bee populations worldwide, and a group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD. This family of viruses employs non-coding RNA sequences, called internal ribosomal entry sites (IRESs), to precisely exploit the host machinery for viral protein production. Using single-particle cryo-electron microscopy (cryo-EM), we have characterized how the IRES of Israeli acute paralysis virus (IAPV) intergenic region captures and redirects translating ribosomes toward viral RNA messages. We reconstituted two in vitro reactions targeting a pre-translocation and a post-translocation state of the IAPV-IRES in the ribosome, allowing us to identify six structures using image processing classification methods. From these, we reconstructed the trajectory of IAPV-IRES from the early small subunit recruitment to the final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. Efforts directed toward fighting CCD by targeting the IAPV-IRES using RNA-interference technology are underway, and the structural framework presented here may assist in further refining these approaches.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Feb 26, 2020Group: Source and taxonomy / Category: entity_src_gen / entity_src_nat
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_nat.common_name ..._entity_src_gen.pdbx_host_org_scientific_name / _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
2: 18S rRNA
B: uS2
C: eS1
D: uS5
E: uS3
F: eS4
G: uS7
H: eS6
I: eS7
J: eS8
K: uS4
L: eS10
M: uS17
N: eS12
O: uS15
P: uS11
Q: uS19
R: uS9
S: eS17
T: uS13
U: eS19
V: uS10
W: eS21
X: uS8
Y: uS12
Z: eS24
a: eS25
b: eS26
c: eS27
d: eS28
e: eS29
f: eS30
g: eS31
h: RACK1
1: IAPV-IRES
5: 28S rRNA
7: 5S rRNA
8: 5.8S rRNA
AA: uL2
AB: uL3
AC: uL4
AD: uL18
AE: eL6
AF: uL30
AG: eL8
AH: uL6
AI: uL16
AJ: uL11
AL: eL13
AM: L14e
AN: eL15
AO: uL13
AP: uL22
AQ: eL18
AR: eL19
AS: eL20
AT: eL21
AU: eL22
AV: uL14
AW: eL24
AX: eL23
AY: uL24
AZ: eL27
Aa: uL15
Ab: eL29
Ac: eL30
Ad: eL31
Ae: eL32
Af: eL33
Ag: eL34
Ah: eL35
Ai: eL36
Aj: eL37
Ak: eL38
Al: eL39
Am: eL40
An: eL41
Ao: eL42
Ap: eL43
Ar: eL28
AK: uL1


Theoretical massNumber of molelcules
Total (without water)3,411,88581
Polymers3,411,88581
Non-polymers00
Water0
1


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

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Components

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RNA chain , 5 types, 5 molecules 21578

#1: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#35: RNA chain IAPV-IRES


Mass: 81572.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cell Free Synthesis. The RNA molecule was made in vitro
Source: (gene. exp.) Israeli acute paralysis virus / Production host: Synthetic construct (others)
#36: RNA chain 28S rRNA / 28S ribosomal RNA


Mass: 1164741.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#37: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#38: RNA chain 5.8S rRNA / 5.8S ribosomal RNA


Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)

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Protein , 75 types, 75 molecules BCDEFGHIJKLMNOPQRSTUVWXYZabcde...

#2: Protein uS2


Mass: 33003.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#3: Protein eS1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#4: Protein uS5


Mass: 27485.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#5: Protein uS3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#6: Protein eS4


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#7: Protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#8: Protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#9: Protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#10: Protein eS8


Mass: 24134.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#11: Protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#12: Protein eS10


Mass: 17156.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3
#13: Protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#14: Protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#15: Protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#16: Protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U472
#17: Protein uS19


Mass: 17049.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#18: Protein uS9


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#19: Protein eS17


Mass: 15552.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#20: Protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#21: Protein eS19


Mass: 16235.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#22: Protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2
#23: Protein eS21


Mass: 9043.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#24: Protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#25: Protein uS12


Mass: 15784.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#26: Protein eS24


Mass: 15548.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#27: Protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#28: Protein eS26


Mass: 12961.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#29: Protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#30: Protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#31: Protein eS29


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#32: Protein eS30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#33: Protein eS31


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#34: Protein RACK1 / Receptor for activated C kinase 1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#39: Protein uL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TT27
#40: Protein uL3


Mass: 45976.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TL06
#41: Protein uL4


Mass: 44232.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVW5
#42: Protein uL18


Mass: 34479.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYJ6
#43: Protein eL6


Mass: 33028.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKF7
#44: Protein uL30


Mass: 29514.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SV32
#45: Protein eL8


Mass: 27655.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1STW0
#46: Protein uL6


Mass: 21871.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TX33, UniProt: G1SWI6*PLUS
#47: Protein uL16


Mass: 24643.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZQ2
#48: Protein uL11


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUB8
#49: Protein eL13


Mass: 24331.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#50: Protein L14e


Mass: 21950.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KNW6
#51: Protein eL15 / List of Subaru engines


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T0C1
#52: Protein uL13


Mass: 23547.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#53: Protein uL22


Mass: 21444.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TVT6
#54: Protein eL18


Mass: 21821.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#55: Protein eL19


Mass: 23480.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJR3
#56: Protein eL20


Mass: 20743.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#57: Protein eL21 /


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHQ2
#58: Protein eL22


Mass: 14936.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TSG1
#59: Protein uL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T6D1
#60: Protein eL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE28
#61: Protein eL23


Mass: 17768.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SE76
#62: Protein uL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SQH0
#63: Protein eL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TXF6
#64: Protein uL15


Mass: 16617.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SNY0
#65: Protein eL29


Mass: 24931.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGR6
#66: Protein eL30


Mass: 12807.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDL2
#67: Protein eL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SHG0
#68: Protein eL32 / CD59


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U437
#69: Protein eL33


Mass: 12580.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SF08
#70: Protein eL34 /


Mass: 14210.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U945
#71: Protein eL35


Mass: 14566.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIT5
#72: Protein eL36


Mass: 12263.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTQ5
#73: Protein eL37


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: U3KPD5
#74: Protein eL38


Mass: 8272.040 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#75: Protein eL39


Mass: 6455.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TTN1
#76: Protein eL40


Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#78: Protein eL42


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U344
#79: Protein eL43


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SY53
#80: Protein eL28


Mass: 15783.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7L1
#81: Protein uL1


Mass: 24879.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SKZ8

-
Protein/peptide , 1 types, 1 molecules An

#77: Protein/peptide eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Structure of a mammalian 80S ribosome in complex with the Israeli Acute Paralysis Virus IRES (Class 2)
Type: RIBOSOME / Entity ID: #1-#81 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMTris-HClTris1
2100 mMKCl1
38 mMMgCl21
42 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Ribosomal complexes for the pre-translocated state were assembled at 240-390 nM concentration and applied to plasma treated holey carbon.
Specimen supportDetails: Plasma cleaning for both holey carbon and holey gold grids was done on a Gatan Solarus with Hydrogen (6.4 sccm gas flow) and Oxygen (27.5 sccm gas flow) and 10 W cleaning power
Grid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot force = 3s Wait time = 15s Drain time = 0s Blot time = 2.5 to 3 s

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 31000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.26 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 42.09 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 11234
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40

-
Processing

EM software
IDNameCategory
2Leginonimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1240275
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40701 / Symmetry type: POINT

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