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- PDB-6w2s: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-I... -

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Basic information

Entry
Database: PDB / ID: 6w2s
TitleStructure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)
Components
  • (Eukaryotic translation initiation factor 3 subunit ...) x 8
  • 18S rRNA18S ribosomal RNA
  • CrPV 5'-UTR IRES
  • RACK1Receptor for activated C kinase 1
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS29
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • uS10
  • uS11
  • uS12
  • uS13
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRibosome/TRANSLATION / CrPV 5'-UTR IRES / Internal ribosome entry site / RIBOSOME / Ribosome-TRANSLATION complex
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / laminin receptor activity / oxidized pyrimidine DNA binding ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / IRES-dependent viral translational initiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / formation of cytoplasmic translation initiation complex / laminin receptor activity / oxidized pyrimidine DNA binding / positive regulation of DNA N-glycosylase activity / positive regulation of base-excision repair / response to TNF agonist / negative regulation of DNA repair / 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 / regulation of translational initiation / NF-kappaB complex / 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 / spindle assembly / positive regulation of JUN kinase activity / isopeptidase activity / ribosomal small subunit biogenesis / translation initiation factor binding / polysome / positive regulation of microtubule polymerization / laminin binding / cellular response to leukemia inhibitory factor / Hsp70 protein binding / translation initiation factor activity / polysomal ribosome / negative regulation of protein ubiquitination / endodeoxyribonuclease activity / positive regulation of interleukin-2 production / ribosomal small subunit assembly / mitotic spindle / ruffle membrane / Hsp90 protein binding / fibrillar center / small ribosomal subunit rRNA binding / chromosome segregation / DNA damage response, detection of DNA damage / PML body / RNA polymerase II transcription regulatory region sequence-specific DNA binding / metallopeptidase activity / rRNA processing / cellular response to hydrogen peroxide / positive regulation of NIK/NF-kappaB signaling / cytoplasmic translation / ribosome binding / cellular response to tumor necrosis factor / thiol-dependent deubiquitinase / 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 / protein deubiquitination / 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 / plasma membrane / metal ion binding / nucleus / cytosol
Ribosomal protein S27a / Ribosomal protein S4/S9 / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Translation initiation factor 3 complex subunit L / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site ...Ribosomal protein S27a / Ribosomal protein S4/S9 / Ribosomal protein S6e, conserved site / Ribosomal protein S8e, conserved site / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Translation initiation factor 3 complex subunit L / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S15P / Ribosomal protein S3, conserved site / Ribosomal protein S19/S15, superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S7 domain / Rpn11/EIF3F, C-terminal / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein S2, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein SA / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit F / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S28e conserved site / Ribosomal protein S5 domain 2-type fold, subgroup / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / K homology domain superfamily, prokaryotic type / S15/NS1, RNA-binding / Eukaryotic translation initiation factor 3 subunit K / Ribosomal protein S13-like, H2TH / Zinc-binding ribosomal protein / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal protein S13/S15, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S5, N-terminal / Ribosomal protein S4e, N-terminal / Ribosomal protein S4e, central region / Ribosomal protein S6, eukaryotic / Ribosomal protein L2, domain 2 / Ribosomal protein S17e, conserved site / WD40/YVTN repeat-like-containing domain superfamily / K homology domain-like, alpha/beta / Armadillo-type fold / Eukaryotic translation initiation factor 3 subunit E / WD40-repeat-containing domain / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17, archaeal/eukaryotic / 50S ribosomal protein L30e-like / Ribosomal protein S12/S23 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S3, C-terminal domain / KH domain / KOW motif / Ribosomal family S4e / 40S ribosomal protein S4 C-terminus / Ribosomal protein S7e / Ribosomal protein S8e / Ribosomal protein S4/S9 N-terminal domain / S4 domain / Plectin/S10 domain / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein S15 / 40S ribosomal protein SA C-terminus / Ribosomal protein S11 / Ribosomal protein S9/S16 / Ribosomal S17 / Ribosomal protein S13/S18 / Ribosomal protein S10p/S20e / Ribosomal protein S8 / Ribosomal protein S12/S23 / Ribosomal protein S24e / S25 ribosomal protein / Ribosomal protein S26e / Ribosomal protein S27 / Ribosomal protein S28e / Ubiquitin family / Ribosomal protein S30
40S ribosomal protein S3 / gb:8895506: / Eukaryotic translation initiation factor 3 subunit M / 40S ribosomal protein S2 / 40S ribosomal protein S7 / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit H / 40S ribosomal protein S3a / 40S ribosomal protein S13 / Eukaryotic translation initiation factor 3 subunit A ...40S ribosomal protein S3 / gb:8895506: / Eukaryotic translation initiation factor 3 subunit M / 40S ribosomal protein S2 / 40S ribosomal protein S7 / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit H / 40S ribosomal protein S3a / 40S ribosomal protein S13 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S24 / 40S ribosomal protein S27a / WD_REPEATS_REGION domain-containing protein / 40S ribosomal protein S20 / Uncharacterized protein / 40S ribosomal protein S12 / Eukaryotic translation initiation factor 3 subunit L / 40S ribosomal protein S9 / 40S ribosomal protein S23 / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / S10_plectin domain-containing protein / 40S ribosomal protein S29 / Uncharacterized protein / 40S ribosomal protein S15 / 40S ribosomal protein S27 / 40S ribosomal protein SA / 40S ribosomal protein S17 / 40S ribosomal protein S11 / 40S ribosomal protein S18 / 40S ribosomal protein S30 / 40S ribosomal protein S19 / 40S ribosomal protein S6 / 40S ribosomal protein S4 / 40S ribosomal protein S8 / 40S ribosomal protein S28 / Ribosomal protein S5 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S15a
Biological speciesCricket paralysis virus
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsNeupane, R. / Pisareva, V. / Rodriguez, C.F. / Pisarev, A. / Fernandez, I.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097014 United States
CitationJournal: Elife / Year: 2020
Title: A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.
Authors: Ritam Neupane / Vera P Pisareva / Carlos F Rodriguez / Andrey V Pisarev / Israel S Fernández /
Abstract: Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have ...Taking control of the cellular apparatus for protein production is a requirement for virus progression. To ensure this control, diverse strategies of cellular mimicry and/or ribosome hijacking have evolved. The initiation stage of translation is especially targeted as it involves multiple steps and the engagement of numerous initiation factors. The use of structured RNA sequences, called nternal ibosomal ntry ites (IRES), in viral RNAs is a widespread strategy for the exploitation of eukaryotic initiation. Using a combination of electron cryo-microscopy (cryo-EM) and reconstituted translation initiation assays with native components, we characterized how a novel IRES at the 5'-UTR of a viral RNA assembles a functional initiation complex via an uAUG intermediate. The IRES features a novel extended, multi-domain architecture, that circles the 40S head. The structures and accompanying functional data illustrate the importance of 5'-UTR regions in translation regulation and underline the relevance of the untapped diversity of viral IRESs.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-21529
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Structure viewerMolecule:
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Assembly

Deposited unit
A: 18S rRNA
0: CrPV 5'-UTR IRES
B: uS2
C: eS1
D: uS5
F: eS4
H: eS6
I: eS7
J: eS8
K: uS4
M: uS17
O: uS15
P: uS11
W: eS21
X: uS8
Y: uS12
Z: eS24
b: eS26
c: eS27
f: eS30
E: uS3
G: uS7
L: eS10
N: eS12
Q: uS19
R: uS9
S: eS17
T: uS13
U: eS19
V: uS10
a: eS25
d: eS28
e: eS29
g: eS31
h: RACK1
1: Eukaryotic translation initiation factor 3 subunit A
2: Eukaryotic translation initiation factor 3 subunit C
3: Eukaryotic translation initiation factor 3 subunit E
4: Eukaryotic translation initiation factor 3 subunit F
5: Eukaryotic translation initiation factor 3 subunit H
6: Eukaryotic translation initiation factor 3 subunit K
7: Eukaryotic translation initiation factor 3 subunit L
8: Eukaryotic translation initiation factor 3 subunit M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,840,04945
Polymers1,839,95943
Non-polymers902
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, Sucrose density gradient analysis, microscopy, Low resolution cryo-EM at 200 kV
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 2 types, 2 molecules A0

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


Mass: 547733.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#2: RNA chain CrPV 5'-UTR IRES


Mass: 121094.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricket paralysis virus / Production host: Escherichia coli (E. coli) / References: GenBank: 8895506

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Protein , 33 types, 33 molecules BCDFHIJKMOPWXYZbcfEGLNQRSTUVad...

#3: Protein uS2 / 40S ribosomal protein SA


Mass: 33022.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TWL4
#4: Protein eS1 / 40S ribosomal protein S3a


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SS70
#5: Protein uS5 / S5 DRBM domain-containing protein


Mass: 27529.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SWM1
#6: Protein eS4 / 40S ribosomal protein S4


Mass: 29596.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#7: Protein eS6 / 40S ribosomal protein S6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#8: Protein eS7 / 40S ribosomal protein S7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#9: Protein eS8 / 40S ribosomal protein S8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#10: Protein uS4 / Ribosomal protein S9


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#11: Protein uS17 / 40S ribosomal protein S11


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#12: Protein uS15 / Ribosomal protein S13


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#13: 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
#14: Protein eS21


Mass: 9098.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
#15: Protein uS8 / Ribosomal protein S15a


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#16: Protein uS12 / Ribosomal protein S23


Mass: 15784.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47
#17: Protein eS24 / 40S ribosomal protein S24


Mass: 15548.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3D8
#18: Protein eS26 / 40S ribosomal protein S26


Mass: 13015.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#19: Protein eS27 / 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#20: Protein eS30 / 40S ribosomal protein S30


Mass: 14498.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#21: Protein uS3 / Ribosomal protein S3


Mass: 31146.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3
#22: Protein uS7 / 40S ribosomal protein S5


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5
#23: 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
#24: Protein eS12 / 40S ribosomal protein S12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#25: 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
#26: Protein uS9 / Ribosomal protein S16


Mass: 19213.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: Protein eS28 / Ribosomal protein S28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#33: 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
#34: Protein eS31 / Ribosomal protein S27a


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#35: 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

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Eukaryotic translation initiation factor 3 subunit ... , 8 types, 8 molecules 12345678

#36: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta


Mass: 164902.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SMZ5
#37: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105706.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1U971
#38: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / eIF-3 p48


Mass: 54199.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SUC8
#39: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37846.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLC2
#40: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3 gamma / eIF3 p40 subunit


Mass: 41083.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1ST95
#41: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / eIF-3 p25


Mass: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T3L2
#42: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 71001.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SED9
#43: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SLW8

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Non-polymers , 2 types, 2 molecules

#44: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#45: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the open state (Class 1)
Type: RIBOSOME / Entity ID: #1-#43 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Grids were blotted for 2.5s and flash cooled in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 8 sec. / Electron dose: 56.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: REFMAC / Version: 5.8.0253 / Classification: refinement
EM software
IDNameCategoryDetails
1Gautomatchparticle selectionno templates, diameter value 260 pixels
2Leginonimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10REFMACmodel refinement
11PHENIXmodel refinement
12RELIONinitial Euler assignment
13RELIONfinal Euler assignment
14RELIONclassification
15RELION3D reconstruction
Image processingDetails: The microscope was equipped with an energy filter with slits aperture of 20eV, installed before the detector.
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 915647
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36100 / Num. of class averages: 1 / Symmetry type: POINT
RefinementResolution: 3→313.91 Å / Cor.coef. Fo:Fc: 0.843 / SU B: 20.39 / SU ML: 0.323 / ESU R: 0.367
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.40504 --
Obs0.40504 1601387 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 120.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.3 Å2-0.07 Å2
2---0.14 Å20.02 Å2
3---0.38 Å2
Refinement stepCycle: 1 / Total: 106817
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.012113071
ELECTRON MICROSCOPYr_bond_other_d0.0030.01882174
ELECTRON MICROSCOPYr_angle_refined_deg1.1721.478162495
ELECTRON MICROSCOPYr_angle_other_deg1.1891.94192580
ELECTRON MICROSCOPYr_dihedral_angle_1_deg8.57957853
ELECTRON MICROSCOPYr_dihedral_angle_2_deg30.39321.0483550
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.2861512304
ELECTRON MICROSCOPYr_dihedral_angle_4_deg16.2415592
ELECTRON MICROSCOPYr_chiral_restr0.0610.216462
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0295213
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0224544
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.9713.64531547
ELECTRON MICROSCOPYr_mcbond_other0.9713.64531546
ELECTRON MICROSCOPYr_mcangle_it1.77620.46439355
ELECTRON MICROSCOPYr_mcangle_other1.77620.46439356
ELECTRON MICROSCOPYr_scbond_it0.76712.53181524
ELECTRON MICROSCOPYr_scbond_other0.76712.53181524
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.38718.746123141
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.057 118423 -
Obs--100 %

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