6W2T

Structure of the Cricket Paralysis Virus 5-UTR IRES (CrPV 5-UTR-IRES) bound to the small ribosomal subunit in the closed state (Class 2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A complex IRES at the 5'-UTR of a viral mRNA assembles a functional 48S complex via an uAUG intermediate.

Neupane, R.Pisareva, V.P.Rodriguez, C.F.Pisarev, A.V.Fernandez, I.S.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.54575
  • Primary Citation of Related Structures:  
    6W2S, 6W2T

  • PubMed 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 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 I nternal R ibosomal E ntry S 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.


  • Organizational Affiliation

    Department of Biological Sciences, Columbia University, New York, United States.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uS2295Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TWL4 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
eS1264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
uS5255Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWM1 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS4E [auth F]263Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS6F [auth H]249Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eS7G [auth I]194Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVB0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS8H [auth J]208Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uS4I [auth K]194Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS17J [auth M]158Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uS15K [auth O]151Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uS11L [auth P]151Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U472 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eS21M [auth W]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uS8N [auth X]130Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uS12O [auth Y]143Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eS24P [auth Z]134Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T3D8 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eS26Q [auth b]115Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TFE8 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS27R [auth c]84Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eS30S [auth f]133Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS3T [auth E]281Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uS7U [auth G]204Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eS10V [auth L]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPV3 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eS12W [auth N]132Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS19X [auth Q]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS9Y [auth R]172Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS17Z [auth S]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS13AA [auth T]152Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS19BA [auth U]145Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uS10CA [auth V]119Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SIZ2 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS25DA [auth i]125Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eS28EA [auth d]69Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS29FA [auth e]56Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eS31GA [auth g]156Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1HA [auth h]317Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EIA [auth 3]462Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SUC8 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FJA [auth 4]364Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KKA [auth 6]218Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T3L2 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LLA [auth 7]607Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SED9 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MMA [auth 8]374Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SLW8 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ANA [auth 1]1,362Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMZ5 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit COA [auth 2]913Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U971 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DPA [auth 9]558Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for K7IM66 (Nasonia vitripennis)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HQA [auth 5]363Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1ST95 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth a]1,697Oryctolagus cuniculus
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Entity ID: 44
MoleculeChains LengthOrganismImage
CrPV 5'-UTR IRESRA [auth A]377Cricket paralysis virus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.36 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097014

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-04-29
    Changes: Database references