9H6Y | pdb_00009h6y

Late-stage 48S Initiation Complex (LS48S IC) guided by the trans-RNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Programmable initiation of mRNA translation by trans-RNA.

Jia, L.Nguyen, T.T.Uematsu, S.Gu, Y.Shi, S.Hashem, Y.Qian, S.B.

(2025) Nat Biotechnol 

  • DOI: https://doi.org/10.1038/s41587-025-02897-1
  • Primary Citation of Related Structures:  
    9H6Y, 9H74

  • PubMed Abstract: 

    Several approaches exist to silence genes, but few tools are available to activate individual mRNAs for translation inside cells. Guiding ribosomes to specific start codons without altering the original sequence remains a formidable task. Here we design capped trans-RNAs capable of directing ribosomes to specific initiation sites on individual mRNAs when the trans-cap is positioned near the target start codon. Structural and biochemical data suggest that the capped trans-RNA facilitates ribosome loading and scanning on the target mRNA through a synergistic mechanism involving alternative cap recognition. The trans-RNA also acts independently of the cap on the target mRNA, enabling translation of circular RNAs lacking internal ribosome entry sites. We apply trans-RNAs in vivo to achieve programmable alternative translation of endogenous genes in mouse liver. Finally, we provide the evidence for the existence of natural transcripts that, similarly to exogenous trans-RNAs, activate translation of endogenous mRNAs.


  • Organizational Affiliation
    • Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1D [auth A]284Oryctolagus cuniculusMutation(s): 0 
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UniProt GroupG1T2G4
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3E [auth B]485Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2F [auth C]295Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1G [auth D]264Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5H [auth E]270Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0AAA9WW19 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3I [auth F]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4J [auth G]263Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7K [auth H]204Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6L [auth I]249Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS7M [auth J]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8N [auth K]208Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4O [auth L]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS10P [auth M]149Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T168 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17Q [auth N]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12R [auth O]132Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15S [auth P]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11T [auth Q]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19U [auth R]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9V [auth S]146Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17W [auth T]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13X [auth U]152Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19Y [auth V]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10Z [auth W]119Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21AA [auth X]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8BA [auth Y]130Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12CA [auth Z]143Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth a]133Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS26EA [auth b]115Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27FA [auth c]84Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28GA [auth d]69Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14HA [auth e]56Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-ribosomal protein eS31 fusion proteinIA [auth f]156Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1JA [auth g]317Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like FUBI-ribosomal protein eS30 fusion proteinKA [auth i]133Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4CLA [auth j]144Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
ATP binding cassette subfamily E member 1MA [auth k]599Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS32NA [auth l]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS25OA [auth n]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5PA [auth o]430Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TGW1 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChains LengthOrganismImage
Initiator methionylated tRNAA [auth 1]76Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth 2]1,863Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
Linear mRNAC [auth 3]160Oryctolagus cuniculus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTISOLDE1.6
MODEL REFINEMENTPHENIX1.20.1-4487
RECONSTRUCTIONcryoSPARC4.5.1

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 StatesDP1GM142101
Howard Hughes Medical Institute (HHMI)United States55108556
European Research Council (ERC)European Union101088541

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release