3JAM

CryoEM structure of 40S-eIF1A-eIF1 complex from yeast


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 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

Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.

Llacer, J.L.Hussain, T.Marler, L.Aitken, C.E.Thakur, A.Lorsch, J.R.Hinnebusch, A.G.Ramakrishnan, V.

(2015) Mol Cell 59: 399-412

  • DOI: https://doi.org/10.1016/j.molcel.2015.06.033
  • Primary Citation of Related Structures:  
    3JAM, 3JAP

  • PubMed Abstract: 

    Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.


  • 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 
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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 
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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 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
uS3E [auth D]237Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eS4F [auth E]261Kluyveromyces lactisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
uS7G [auth F]227Kluyveromyces lactisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
eS6H [auth G]236Kluyveromyces lactisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
eS7I [auth H]190Kluyveromyces lactisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
eS8J [auth I]201Kluyveromyces lactisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
uS4K [auth J]188Kluyveromyces lactisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
eS10L [auth K]106Kluyveromyces lactisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uS17M [auth L]156Kluyveromyces lactisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eS12N [auth M]134Kluyveromyces lactisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
uS15O [auth N]151Kluyveromyces lactisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
uS11P [auth O]137Kluyveromyces lactisMutation(s): 0 
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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: 17
MoleculeChains Sequence LengthOrganismDetailsImage
uS19Q [auth P]142Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
uS9R [auth Q]143Kluyveromyces lactisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eS17S [auth R]136Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWU3 (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
uS13T [auth S]146Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CWT9 (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
eS19U [auth T]144Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uS10V [auth U]117Kluyveromyces lactisMutation(s): 0 
UniProt
Find proteins for Q6CIM1 (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
eS21W [auth V]87Kluyveromyces lactisMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
uS8X [auth W]130Kluyveromyces lactisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uS12Y [auth X]145Kluyveromyces lactisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eS24Z [auth Y]135Kluyveromyces lactisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
eS25AA [auth Z]108Kluyveromyces lactisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
eS26BA [auth a]119Kluyveromyces lactisMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eS27CA [auth b]82Kluyveromyces lactisMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
eS28DA [auth c]67Kluyveromyces lactisMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
uS14EA [auth d]56Kluyveromyces lactisMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eS30FA [auth e]63Kluyveromyces 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 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL41IA [auth h]25Kluyveromyces lactisMutation(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 
MD [auth a],
ND [auth b],
PD [auth f]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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],
LA [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth J],
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],
OD [auth f],
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: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    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