5K0Y

m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 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

eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.

Simonetti, A.Brito Querido, J.Myasnikov, A.G.Mancera-Martinez, E.Renaud, A.Kuhn, L.Hashem, Y.

(2016) Mol.Cell 63: 206-217

  • DOI: 10.1016/j.molcel.2016.05.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accomm ...

    mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.


    Organizational Affiliation

    CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France. Electronic address: a.simonetti@ibmc-cnrs.unistra.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 2 subunit 1
P
266Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S1
Find proteins for G1T2G4 (Oryctolagus cuniculus)
Go to Gene View: EIF2S1
Go to UniProtKB:  G1T2G4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS17
G
158Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100347468
Find proteins for G1TRM4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TRM4
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS9
H
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS16
Find proteins for G1SGX4 (Oryctolagus cuniculus)
Go to Gene View: RPS16
Go to UniProtKB:  G1SGX4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4
I
263Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100338112
Find proteins for G1TK17 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TK17
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS14
J
53Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100337712
Find proteins for G1U7M4 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U7M4
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S9 (Predicted)
K
182Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS9
Find proteins for B7NZS8 (Oryctolagus cuniculus)
Go to Gene View: RPS9
Go to UniProtKB:  B7NZS8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS13
L
137Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100356144
Find proteins for G1TPG3 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TPG3
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit G
M
38Homo sapiensMutation(s): 0 
Gene Names: EIF3G (EIF3S4)
Find proteins for O75821 (Homo sapiens)
Go to Gene View: EIF3G
Go to UniProtKB:  O75821
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit G
O
77Homo sapiensMutation(s): 0 
Gene Names: EIF3G (EIF3S4)
Find proteins for O75821 (Homo sapiens)
Go to Gene View: EIF3G
Go to UniProtKB:  O75821
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS12
Q
142Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS23
Find proteins for G1SZ47 (Oryctolagus cuniculus)
Go to Gene View: RPS23
Go to UniProtKB:  G1SZ47
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS19
R
141Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345774
Find proteins for G1TN62 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TN62
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
eukaryotic initiation factor 2 Gamma subunit (eIF2-Gamma)
S
422Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF2S3
Find proteins for G1SRA8 (Oryctolagus cuniculus)
Go to Gene View: EIF2S3
Go to UniProtKB:  G1SRA8
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 3 subunit I
T
329Oryctolagus cuniculusMutation(s): 0 
Gene Names: EIF3I (EIF3S2)
Find proteins for Q5IH81 (Oryctolagus cuniculus)
Go to Gene View: EIF3I
Go to UniProtKB:  Q5IH81
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS7
U
191Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS5
Find proteins for U3KMN4 (Oryctolagus cuniculus)
Go to Gene View: RPS5
Go to UniProtKB:  U3KMN4
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS30
V
59Oryctolagus cuniculusMutation(s): 0 
Gene Names: FAU
Find proteins for G1T8A2 (Oryctolagus cuniculus)
Go to Gene View: FAU
Go to UniProtKB:  G1T8A2
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS25
W
75Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS25
Find proteins for G1TDB3 (Oryctolagus cuniculus)
Go to Gene View: RPS25
Go to UniProtKB:  G1TDB3
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS7
X
190Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS7
Find proteins for G1SVB0 (Oryctolagus cuniculus)
Go to Gene View: RPS7
Go to UniProtKB:  G1SVB0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27
Y
84Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100345694 (LOC100345044, LOC100348261, RPS27)
Find proteins for G1TZ76 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TZ76
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS15
Z
150Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS13
Find proteins for G1SP51 (Oryctolagus cuniculus)
Go to Gene View: RPS13
Go to UniProtKB:  G1SP51
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS8
a
129Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS15A
Find proteins for G1TG89 (Oryctolagus cuniculus)
Go to Gene View: RPS15A
Go to UniProtKB:  G1TG89
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21
b
82Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS21
Find proteins for G1TM82 (Oryctolagus cuniculus)
Go to Gene View: RPS21
Go to UniProtKB:  G1TM82
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS5
c
226Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TUT9 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TUT9
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
eukaryotic initiation factor 2 subunit Beta (eIF2-Beta)
d
17Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)Mutation(s): 0 
Gene Names: eif2b (aif2b)
Find proteins for Q97W59 (Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Go to UniProtKB:  Q97W59
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS17
e
126Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS17
Find proteins for G1TU13 (Oryctolagus cuniculus)
Go to Gene View: RPS17
Go to UniProtKB:  G1TU13
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS2
f
208Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPSA (LOC100340199)
Find proteins for G1TWL4 (Oryctolagus cuniculus)
Go to Gene View: RPSA
Go to UniProtKB:  G1TWL4
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS3
g
227Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3
Find proteins for G1TNM3 (Oryctolagus cuniculus)
Go to Gene View: RPS3
Go to UniProtKB:  G1TNM3
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS10
h
104Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100341365
Find proteins for G1SIZ2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SIZ2
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS1
i
215Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS3A
Find proteins for G1TN72 (Oryctolagus cuniculus)
Go to Gene View: RPS3A
Go to UniProtKB:  G1TN72
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS11
j
136Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS14
Find proteins for G1T1F0 (Oryctolagus cuniculus)
Go to Gene View: RPS14
Go to UniProtKB:  G1T1F0
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS26
k
99Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100346996
Find proteins for G1TFE8 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TFE8
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS28
l
64Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS28
Find proteins for G1TIB4 (Oryctolagus cuniculus)
Go to Gene View: RPS28
Go to UniProtKB:  G1TIB4
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RACK1
m
313Oryctolagus cuniculusMutation(s): 0 
Gene Names: RACK1
Find proteins for G1SJB4 (Oryctolagus cuniculus)
Go to Gene View: RACK1
Go to UniProtKB:  G1SJB4
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein uS19
n
127Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC103349305
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
Go to UniProtKB:  G1U0Q2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8
o
206Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100352057
Find proteins for G1TJW1 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TJW1
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS31
p
71Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100348379
Find proteins for G1SK22 (Oryctolagus cuniculus)
Go to UniProtKB:  G1SK22
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6
q
237Oryctolagus cuniculusMutation(s): 0 
Gene Names: LOC100339133 (RPS6)
Find proteins for G1TM55 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TM55
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12
r
124Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS12
Find proteins for G1SFR8 (Oryctolagus cuniculus)
Go to Gene View: RPS12
Go to UniProtKB:  G1SFR8
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24
s
131Oryctolagus cuniculusMutation(s): 0 
Find proteins for G1TS40 (Oryctolagus cuniculus)
Go to UniProtKB:  G1TS40
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein eS10
t
98Oryctolagus cuniculusMutation(s): 0 
Gene Names: RPS10
Find proteins for G1T168 (Oryctolagus cuniculus)
Go to Gene View: RPS10
Go to UniProtKB:  G1T168
Entity ID: 1
MoleculeChainsLengthOrganism
tRNAN75Oryctolagus cuniculus
Entity ID: 2
MoleculeChainsLengthOrganism
18S ribosomal RNAA1776Oryctolagus cuniculus
Entity ID: 3
MoleculeChainsLengthOrganism
mRNAF30Oryctolagus cuniculus
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceatRAction program ANR CryoEM80S
French National Research AgencyFranceANR-10-LABX-0036_NETRNA

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references
  • Version 1.2: 2017-08-02
    Type: Data collection, Derived calculations
  • Version 1.3: 2018-04-18
    Type: Data collection, Structure summary