3J81

CryoEM structure of a partial yeast 48S preinitiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 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:  

  • 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

    Laboratory of Gene Regulation and Development, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address: ramak@mrc-lmb.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice K. Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
uS2
A
254Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS0
Find proteins for Q6CN12 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CN12
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
eS1
B
255Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS1
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CWD0
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
uS5
C
259Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CKL3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CKL3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
uS3
D
237Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CRK7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
eS4
E
261Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CWJ2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
uS7
F
227Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CRA3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
eS6
G
236Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS6
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS6
Go to UniProtKB:  Q6CM04
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
eS7
H
190Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CTD6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CTD6
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
eS8
I
201Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CMG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CMG3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
uS4
J
188Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CM18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CM18
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
eS10
K
106Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CVZ5
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
uS17
L
156Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CX80
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
eS12
M
134Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CLU4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
uS15
N
151Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CJK0
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
uS11
O
137Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS14 (CRY1)
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS14
Go to UniProtKB:  P27069
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
uS19
P
140Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CKV4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CKV4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
uS9
Q
143Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS16
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS16
Go to UniProtKB:  Q875N2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
eS17
R
136Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CWU3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
uS13
S
146Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CWT9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
eS19
T
144Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CXM0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
uS10
U
117Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CIM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CIM1
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
eS21
V
87Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS21
Find proteins for Q6CXT6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS21
Go to UniProtKB:  Q6CXT6
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
uS8
W
130Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS22
Find proteins for Q6CW21 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CW21
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
uS12
X
145Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for F2Z602 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  F2Z602
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eS24
Y
135Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CU44 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CU44
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
eS25
Z
108Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CW78 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CW78
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
eS26
a
119Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CS01 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CS01
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
eS27
b
82Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CNL2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CNL2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
eS28
c
67Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS28
Find proteins for P33285 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS28
Go to UniProtKB:  P33285
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
eS31
f
150Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: ubi3
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  P69061
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
RACK1
g
326Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CNI7
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
uS14
d
56Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Gene Names: RPS29
Find proteins for Q6CPG3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to Gene View: RPS29
Go to UniProtKB:  Q6CPG3
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
eS30
e
63Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)Mutation(s): 0 
Find proteins for Q6CUH5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
Go to UniProtKB:  Q6CUH5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
eL41
h
25Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL41A (RPL47A, YL41A)
Find proteins for P0CX86 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX86
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
eIF1A
i
153Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TIF11
Find proteins for P38912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38912
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
eIF2 alpha
j
300Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUI2 (TIF211)
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20459
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
eIF1
m
108Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUI1 (RFR1)
Find proteins for P32911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32911
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
eIF2 gamma
k
527Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GCD11 (TIF213)
Find proteins for P32481 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32481
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
eIF2 beta
l
285Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SUI3 (TIF212)
Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P09064
Entity ID: 1
MoleculeChainsLengthOrganism
18S rRNA21799Kluyveromyces lactis
Entity ID: 36
MoleculeChainsLengthOrganism
Met-tRNAi175N/A
Entity ID: 37
MoleculeChainsLengthOrganism
mRNA325synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
MET
Query on MET

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k
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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