3J81

CryoEM structure of a partial yeast 48S preinitiation complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural changes enable start codon recognition by the eukaryotic translation initiation complex.

Hussain, T., Llacer, J.L., Fernandez, I.S., Munoz, A., Martin-Marcos, P., Savva, C.G., Lorsch, J.R., Hinnebusch, A.G., Ramakrishnan, V.

(2014) Cell 159: 597-607

  • DOI: 10.1016/j.cell.2014.10.001
  • Primary Citation of Related Structures:  
    3J81, 3J80

  • PubMed Abstract: 

    • During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought ...

    During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon.

    Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
uS2A254Kluyveromyces lactisMutation(s): 0 
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eS1B255Kluyveromyces lactisMutation(s): 0 
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uS5C259Kluyveromyces lactisMutation(s): 0 
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Entity ID: 5
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uS3D237Kluyveromyces lactisMutation(s): 0 
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Entity ID: 6
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eS4E261Kluyveromyces lactisMutation(s): 0 
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Entity ID: 7
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uS7F227Kluyveromyces lactisMutation(s): 0 
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eS6G236Kluyveromyces lactisMutation(s): 0 
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eS7H190Kluyveromyces lactisMutation(s): 0 
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eS8I201Kluyveromyces lactisMutation(s): 0 
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uS4J188Kluyveromyces lactisMutation(s): 0 
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eS10K106Kluyveromyces lactisMutation(s): 0 
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uS17L156Kluyveromyces lactisMutation(s): 0 
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eS12M134Kluyveromyces lactisMutation(s): 0 
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uS15N151Kluyveromyces lactisMutation(s): 0 
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uS11O137Kluyveromyces lactisMutation(s): 0 
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uS19P140Kluyveromyces lactisMutation(s): 0 
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uS9Q143Kluyveromyces lactisMutation(s): 0 
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eS17R136Kluyveromyces lactisMutation(s): 0 
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uS13S146Kluyveromyces lactisMutation(s): 0 
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eS19T144Kluyveromyces lactisMutation(s): 0 
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uS10U117Kluyveromyces lactisMutation(s): 0 
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eS21V87Kluyveromyces lactisMutation(s): 0 
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uS8W130Kluyveromyces lactisMutation(s): 0 
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uS12X145Kluyveromyces lactisMutation(s): 0 
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eS24Y135Kluyveromyces lactisMutation(s): 0 
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eS25Z108Kluyveromyces lactisMutation(s): 0 
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eS26a119Kluyveromyces lactisMutation(s): 0 
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eS27b82Kluyveromyces lactisMutation(s): 0 
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eS28c67Kluyveromyces lactisMutation(s): 0 
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eS31f150Kluyveromyces lactisMutation(s): 0 
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RACK1g326Kluyveromyces lactisMutation(s): 0 
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uS14d56Kluyveromyces lactisMutation(s): 0 
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eS30e63Kluyveromyces lactisMutation(s): 0 
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eL41h25Saccharomyces cerevisiaeMutation(s): 0 
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eIF1Ai153Saccharomyces cerevisiaeMutation(s): 0 
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eIF2 alphaj300Saccharomyces cerevisiaeMutation(s): 0 
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eIF1m108Saccharomyces cerevisiaeMutation(s): 0 
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eIF2 gammak527Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5.3
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eIF2 betal285Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChainsLengthOrganismImage
18S rRNA21799Kluyveromyces lactis
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Met-tRNAi175N/A
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MoleculeChainsLengthOrganismImage
mRNA325synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MET
Query on MET
Download Ideal Coordinates CCD File 
k
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N		 Ligand Interaction
ZN
Query on ZN
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a, b, f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
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2, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-12-24
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Data collection