3J80

CryoEM structure of 40S-eIF1-eIF1A preinitiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 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 to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit ...

    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
uS2B [auth A]254Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 3
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eS1C [auth B]255Kluyveromyces lactisMutation(s): 0 
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 4
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uS5D [auth C]259Kluyveromyces lactisMutation(s): 0 
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Entity ID: 5
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eS4E261Kluyveromyces lactisMutation(s): 0 
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Entity ID: 6
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eS6F [auth G]236Kluyveromyces lactisMutation(s): 0 
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Entity ID: 7
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eS7G [auth H]190Kluyveromyces lactisMutation(s): 0 
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eS8H [auth I]201Kluyveromyces lactisMutation(s): 0 
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uS4I [auth J]188Kluyveromyces lactisMutation(s): 0 
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uS17J [auth L]156Kluyveromyces lactisMutation(s): 0 
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uS15K [auth N]151Kluyveromyces lactisMutation(s): 0 
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uS11L [auth O]137Kluyveromyces lactisMutation(s): 0 
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eS21M [auth V]87Kluyveromyces lactisMutation(s): 0 
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uS8N [auth W]130Kluyveromyces lactisMutation(s): 0 
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uS12O [auth X]145Kluyveromyces lactisMutation(s): 0 
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Entity ID: 16
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eS24P [auth Y]135Kluyveromyces lactisMutation(s): 0 
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eS26Q [auth a]119Kluyveromyces lactisMutation(s): 0 
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eS27R [auth b]82Kluyveromyces lactisMutation(s): 0 
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eS30S [auth e]63Kluyveromyces lactisMutation(s): 0 
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Entity ID: 20
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uS3T [auth D]237Kluyveromyces lactisMutation(s): 0 
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Entity ID: 21
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uS7U [auth F]227Kluyveromyces lactisMutation(s): 0 
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Entity ID: 22
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eS10V [auth K]106Kluyveromyces lactisMutation(s): 0 
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eS12W [auth M]134Kluyveromyces lactisMutation(s): 0 
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uS19X [auth P]140Kluyveromyces lactisMutation(s): 0 
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uS9Y [auth Q]143Kluyveromyces lactisMutation(s): 0 
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eS17Z [auth R]136Kluyveromyces lactisMutation(s): 0 
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uS13AA [auth S]146Kluyveromyces lactisMutation(s): 0 
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Entity ID: 28
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eS19BA [auth T]144Kluyveromyces lactisMutation(s): 0 
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uS10CA [auth U]117Kluyveromyces lactisMutation(s): 0 
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eS25DA [auth Z]108Kluyveromyces lactisMutation(s): 0 
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eS28EA [auth c]67Kluyveromyces lactisMutation(s): 0 
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uS14FA [auth d]56Kluyveromyces lactisMutation(s): 0 
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eS31GA [auth f]150Kluyveromyces lactisMutation(s): 0 
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RACK1HA [auth g]326Kluyveromyces lactisMutation(s): 0 
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eL41IA [auth h]25Saccharomyces cerevisiaeMutation(s): 0 
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eIF1AJA [auth i]153Saccharomyces cerevisiaeMutation(s): 0 
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eIF1KA [auth j]108Saccharomyces cerevisiaeMutation(s): 0 
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MoleculeChainsLengthOrganismImage
18S rRNAA [auth 2]1799Kluyveromyces lactis
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AD [auth a], BD [auth b], CD [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth 2] , AC [auth 2] , BB [auth 2] , BC [auth 2] , CB [auth 2] , CC [auth 2] , DB [auth 2] , DC [auth 2] , 
AB [auth 2],  AC [auth 2],  BB [auth 2],  BC [auth 2],  CB [auth 2],  CC [auth 2],  DB [auth 2],  DC [auth 2],  EB [auth 2],  EC [auth 2],  FB [auth 2],  FC [auth 2],  GB [auth 2],  GC [auth 2],  HB [auth 2],  HC [auth 2],  IB [auth 2],  IC [auth 2],  JB [auth 2],  JC [auth 2],  KB [auth 2],  KC [auth 2],  LA [auth 2],  LB [auth 2],  LC [auth 2],  MA [auth 2],  MB [auth 2],  MC [auth 2],  NA [auth 2],  NB [auth 2],  NC [auth 2],  OA [auth 2],  OB [auth 2],  OC [auth 2],  PA [auth 2],  PB [auth 2],  PC [auth 2],  QA [auth 2],  QB [auth 2],  QC [auth 2],  RA [auth 2],  RB [auth 2],  RC [auth 2],  SA [auth 2],  SB [auth 2],  SC [auth 2],  TA [auth 2],  TB [auth 2],  TC [auth 2],  UA [auth 2],  UB [auth 2],  UC [auth 2],  VA [auth 2],  VB [auth 2],  VC [auth 2],  WA [auth 2],  WB [auth 2],  WC [auth 2],  XA [auth 2],  XB [auth 2],  XC [auth 2],  YA [auth 2],  YB [auth 2],  YC [auth 2],  ZA [auth 2],  ZB [auth 2],  ZC [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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