8P03

48S late-stage initiation complex with m6A mRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

N 6 -methyladenosine in 5' UTR does not promote translation initiation.

Guca, E.Alarcon, R.Palo, M.Z.Santos, L.Alonso-Gil, S.Davyt, M.de Lima, L.H.F.Boissier, F.Das, S.Zagrovic, B.Puglisi, J.D.Hashem, Y.Ignatova, Z.

(2024) Mol Cell 84: 584-595.e6

  • DOI: https://doi.org/10.1016/j.molcel.2023.12.028
  • Primary Citation of Related Structures:  
    8P03, 8P09

  • PubMed Abstract: 

    The most abundant N 6 -methyladenosine (m 6 A) modification on mRNAs is installed non-stoichiometrically across transcripts, with 5' untranslated regions (5' UTRs) being the least conductive. 5' UTRs are essential for translation initiation, yet the molecular mechanisms orchestrated by m 6 A remain poorly understood. Here, we combined structural, biochemical, and single-molecule approaches and show that at the most common position, a single m 6 A does not affect translation yields, the kinetics of translation initiation complex assembly, or start codon recognition both under permissive growth and following exposure to oxidative stress. Cryoelectron microscopy (cryo-EM) structures of the late preinitiation complex reveal that m 6 A purine ring established stacking interactions with an arginine side chain of the initiation factor eIF2α, although with only a marginal energy contribution, as estimated computationally. These findings provide molecular insights into m 6 A interactions with the initiation complex and suggest that the subtle stabilization is unlikely to affect the translation dynamics under homeostatic conditions or stress.


  • Organizational Affiliation

    INSERM U1212 Acides nucléiques: Régulations Naturelle et Artificielle (ARNA), Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1D [auth A]284Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAE [auth C]207Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS1F [auth D]215Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2G [auth E]270Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3H [auth F]227Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4I [auth G]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5J [auth H]191Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6K [auth I]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5K1UJS7 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS7L [auth J]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8M [auth K]206Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9N [auth L]194Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS10O [auth M]98Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11P [auth N]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12Q [auth O]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15R [auth P]150Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS11S [auth Q]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19T [auth R]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS9U [auth S]141Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17V [auth T]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS13W [auth U]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS19X [auth V]141Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10Y [auth W]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Z [auth X]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aAA [auth Y]130Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23BA [auth Z]143Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CA [auth a]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26DA [auth b]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27EA [auth c]84Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth d]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth e]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS31HA [auth f]71Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein RACK1IA [auth g]313Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30JA [auth i]133Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4CKA [auth j]111Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
ATP binding cassette subfamily E member 1LA [auth k]595Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41MA [auth l]25Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25NA [auth n]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
initiator methionylated tRNAA [auth 1]75Oryctolagus cuniculus
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth 2]1,863Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
m6A-methylated mRNAC [auth 3]9Oryctolagus cuniculus
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 2]
AC [auth 2]
AD [auth 2]
AE [auth 2]
AF [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
AE [auth 2],
AF [auth 2],
AG [auth 2],
AH [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
BE [auth 2],
BF [auth 2],
BG [auth 2],
BH [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth 2],
CF [auth 2],
CG [auth 2],
CH [auth 2],
DB [auth 2],
DC [auth 2],
DD [auth 2],
DE [auth 2],
DF [auth 2],
DG [auth 2],
DH [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
EE [auth 2],
EF [auth 2],
EG [auth 2],
EH [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
FE [auth 2],
FF [auth 2],
FG [auth 2],
FH [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
GE [auth 2],
GF [auth 2],
GG [auth 2],
GH [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
HE [auth 2],
HF [auth 2],
HG [auth 2],
HH [auth 3],
IB [auth 2],
IC [auth 2],
ID [auth 2],
IE [auth 2],
IF [auth 2],
IG [auth 2],
IH [auth I],
JB [auth 2],
JC [auth 2],
JD [auth 2],
JE [auth 2],
JF [auth 2],
JG [auth 2],
JH [auth Z],
KB [auth 2],
KC [auth 2],
KD [auth 2],
KE [auth 2],
KF [auth 2],
KG [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
LE [auth 2],
LF [auth 2],
LG [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
ME [auth 2],
MF [auth 2],
MG [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
NE [auth 2],
NF [auth 2],
NG [auth 2],
OA [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
OE [auth 2],
OF [auth 2],
OG [auth 2],
PA [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
PE [auth 2],
PF [auth 2],
PG [auth 2],
QA [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
QE [auth 2],
QF [auth 2],
QG [auth 2],
RA [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
RE [auth 2],
RF [auth 2],
RG [auth 2],
SA [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
SE [auth 2],
SF [auth 2],
SG [auth 2],
TA [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
TE [auth 2],
TF [auth 2],
TG [auth 2],
UA [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth 2],
UE [auth 2],
UF [auth 2],
UG [auth 2],
VA [auth 2],
VB [auth 2],
VC [auth 2],
VD [auth 2],
VE [auth 2],
VF [auth 2],
VG [auth 2],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth 2],
WE [auth 2],
WF [auth 2],
WG [auth 2],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth 2],
XE [auth 2],
XF [auth 2],
XG [auth 2],
YA [auth 2],
YB [auth 2],
YC [auth 2],
YD [auth 2],
YE [auth 2],
YF [auth 2],
YG [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth 2],
ZE [auth 2],
ZF [auth 2],
ZG [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection