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 1.3 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. 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.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uS2B [auth A]254Kluyveromyces lactisMutation(s): 0 
UniProt
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
MoleculeChains Sequence LengthOrganismDetailsImage
eS1C [auth B]255Kluyveromyces lactisMutation(s): 0 
UniProt
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
MoleculeChains Sequence LengthOrganismDetailsImage
uS5D [auth C]259Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CKL3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
eS4261Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS6F [auth G]236Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eS7G [auth H]190Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS8H [auth I]201Kluyveromyces lactisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uS4I [auth J]188Kluyveromyces lactisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uS17J [auth L]156Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uS15K [auth N]151Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uS11L [auth O]137Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eS21M [auth V]87Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uS8N [auth W]130Kluyveromyces lactisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uS12O [auth X]145Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for F2Z602 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eS24P [auth Y]135Kluyveromyces lactisMutation(s): 0 
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Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eS26Q [auth a]119Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eS27R [auth b]82Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eS30S [auth e]63Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
uS3T [auth D]237Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
uS7U [auth F]227Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
eS10V [auth K]106Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
eS12W [auth M]134Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS19X [auth P]140Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS9Y [auth Q]143Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS17Z [auth R]136Kluyveromyces lactisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS13AA [auth S]146Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS19BA [auth T]144Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
uS10CA [auth U]117Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS25DA [auth Z]108Kluyveromyces lactisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
eS28EA [auth c]67Kluyveromyces lactisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
uS14FA [auth d]56Kluyveromyces lactisMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eS31GA [auth f]150Kluyveromyces lactisMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1HA [auth g]326Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL41IA [auth h]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eIF1AJA [auth i]153Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eIF1KA [auth j]108Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S rRNAA [auth 2]1,799Kluyveromyces lactis
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Small Molecules
Ligands 2 Unique
IDChains Name / 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
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
BB [auth 2]
BC [auth 2]
CB [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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN2
RECONSTRUCTIONRELION

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
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description