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

  • 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.



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uS2B [auth A]254Kluyveromyces lactisMutation(s): 0 
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eS1C [auth B]255Kluyveromyces lactisMutation(s): 0 
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uS5D [auth C]259Kluyveromyces lactisMutation(s): 0 
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uS3E [auth D]237Kluyveromyces lactisMutation(s): 0 
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eS4F [auth E]261Kluyveromyces lactisMutation(s): 0 
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uS7G [auth F]227Kluyveromyces lactisMutation(s): 0 
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eS6H [auth G]236Kluyveromyces lactisMutation(s): 0 
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eS7I [auth H]190Kluyveromyces lactisMutation(s): 0 
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eS10L [auth K]106Kluyveromyces lactisMutation(s): 0 
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uS17M [auth L]156Kluyveromyces lactisMutation(s): 0 
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eS12N [auth M]134Kluyveromyces lactisMutation(s): 0 
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uS11P [auth O]137Kluyveromyces lactisMutation(s): 0 
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uS19Q [auth P]140Kluyveromyces lactisMutation(s): 0 
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uS9R [auth Q]143Kluyveromyces lactisMutation(s): 0 
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eS17S [auth R]136Kluyveromyces lactisMutation(s): 0 
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uS13T [auth S]146Kluyveromyces lactisMutation(s): 0 
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eS19U [auth T]144Kluyveromyces lactisMutation(s): 0 
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uS10V [auth U]117Kluyveromyces lactisMutation(s): 0 
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eS21W [auth V]87Kluyveromyces lactisMutation(s): 0 
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eS26BA [auth a]119Kluyveromyces lactisMutation(s): 0 
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eS27CA [auth b]82Kluyveromyces lactisMutation(s): 0 
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eS28DA [auth c]67Kluyveromyces lactisMutation(s): 0 
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eS31EA [auth f]150Kluyveromyces lactisMutation(s): 0 
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RACK1FA [auth g]326Kluyveromyces lactisMutation(s): 0 
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uS14GA [auth d]56Kluyveromyces lactisMutation(s): 0 
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eS30HA [auth e]63Kluyveromyces lactisMutation(s): 0 
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eL41IA [auth h]25Saccharomyces cerevisiaeMutation(s): 0 
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eIF1ALA [auth i]153Saccharomyces cerevisiaeMutation(s): 0 
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eIF2 alphaMA [auth j]300Saccharomyces cerevisiaeMutation(s): 0 
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eIF1NA [auth m]108Saccharomyces cerevisiaeMutation(s): 0 
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eIF2 gammaOA [auth k]527Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.5.3
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eIF2 betaPA [auth l]285Saccharomyces cerevisiaeMutation(s): 0 
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18S rRNAA [auth 2]1,799Kluyveromyces lactis
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Met-tRNAiJA [auth 1]75N/A
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mRNAKA [auth 3]25synthetic construct
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MET
Query on MET
Download Ideal Coordinates CCD File 
WD [auth k]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
TD [auth a],
UD [auth b],
VD [auth f]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AB [auth 2],
AC [auth 2],
AD [auth 2],
BB [auth 2],
BC [auth 2],
AB [auth 2],
AC [auth 2],
AD [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
QA [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
RA [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
SA [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth G],
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: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
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