6W2S

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)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 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: 10.7554/eLife.54575
  • Structures With Same Primary Citation

  • 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 espe ...

    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 Biochemistry and Molecular Biophysics, Columbia University, New York, United States.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
uS2B295Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSALOC100340199
Find proteins for G1TWL4 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
eS1C264Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3ALOC100342838LOC100348981
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uS5D255Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
eS4F263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
eS6H249Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS7I194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eS8J208Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
uS4K194Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uS17M158Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS11
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eS21W83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uS8X130Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uS12Y143Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
eS24Z134Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS24
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eS27c84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694LOC100345044LOC100348261RPS27
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
eS30f133Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uS7G204Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eS10L149Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348511
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
eS12N132Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
uS19Q145Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
uS9R172Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eS17S135Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100353606RPS17
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
uS13T152Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS18
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eS19U145Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
uS10V119Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS20LOC100341365LOC100348955LOC100354063
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
eS29e56Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
RACK1h317Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit A11362Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3AEIF3S10
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit C2913Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3CEIF3S8LOC100344472
Find proteins for G1U971 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit E3462Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3EEIF3S6INT6
Find proteins for G1SUC8 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit F4364Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3FEIF3S5
Find proteins for G1SLC2 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit H5363Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3HEIF3S3
Find proteins for G1ST95 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit K6218Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3KEIF3S12
Find proteins for G1T3L2 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit L7607Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3LEIF3EIPEIF3S6IP
Find proteins for G1SED9 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit M8374Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3M
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
uS15O151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uS11P151Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337691
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
eS26b115Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
uS3E281Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eS25a125Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
eS28d69Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eS31g156Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNAA1697Oryctolagus cuniculus

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Entity ID: 2
MoleculeChainsLengthOrganism
CrPV 5'-UTR IRES0377Cricket paralysis virus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
b
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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 

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