8PJ2

Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for translational control by the human 48S initiation complex.

Petrychenko, V.Yi, S.H.Liedtke, D.Peng, B.Z.Rodnina, M.V.Fischer, N.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01378-4
  • Primary Citation of Related Structures:  
    8PJ1, 8PJ2, 8PJ3, 8PJ4, 8PJ5, 8PJ6, 8RG0

  • PubMed Abstract: 

    The selection of an open reading frame (ORF) for translation of eukaryotic mRNA relies on remodeling of the scanning 48S initiation complex into an elongation-ready 80S ribosome. Using cryo-electron microscopy, we visualize the key commitment steps orchestrating 48S remodeling in humans. The mRNA Kozak sequence facilitates mRNA scanning in the 48S open state and stabilizes the 48S closed state by organizing the contacts of eukaryotic initiation factors (eIFs) and ribosomal proteins and by reconfiguring mRNA structure. GTPase-triggered large-scale fluctuations of 48S-bound eIF2 facilitate eIF5B recruitment, transfer of initiator tRNA from eIF2 to eIF5B and the release of eIF5 and eIF2. The 48S-bound multisubunit eIF3 complex controls ribosomal subunit joining by coupling eIF exchange to gradual displacement of the eIF3c N-terminal domain from the intersubunit interface. These findings reveal the structural mechanism of ORF selection in human cells and explain how eIF3 could function in the context of the 80S ribosome.


  • Organizational Affiliation

    Project Group Molecular Machines in Motion, Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BA [auth 1]814Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106263 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IB [auth 2]325Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000084623 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KC [auth 3]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000178982 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FD [auth 4]357Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000175390 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LE [auth 5]564Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MF [auth 6]374Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149100 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HH [auth 8]352Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147677 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41I [auth 9]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth B]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformL [auth C]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9M [auth D]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23N [auth E]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30O [auth F]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7P [auth G]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27Q [auth H]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13R [auth I]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aS [auth J]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21T [auth K]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2U [auth L]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17V [auth M]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAW [auth N]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aX [auth O]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14Y [auth P]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26Z [auth Q]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8AA [auth R]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6BA [auth S]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CA [auth T]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5DA [auth V]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16EA [auth Y]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3FA [auth Z]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10GA [auth a]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15HA [auth b]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1IA [auth c]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19JA [auth d]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25KA [auth e]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18LA [auth f]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20MA [auth h]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29NA [auth i]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinOA [auth k]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12PA [auth m]132Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112306 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28QA [auth n]69Homo sapiensMutation(s): 0 
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PHAROS:  P62857
GTEx:  ENSG00000233927 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GRA [auth o]320Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130811 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1A, X-chromosomalSA [auth q]144Homo sapiensMutation(s): 0 
Gene Names: EIF1AXEIF1AEIF4C
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GTEx:  ENSG00000173674 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1TA [auth r]315Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134001 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 3UA [auth t]472Homo sapiensMutation(s): 0 
EC: 3.6.5.3
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GTEx:  ENSG00000130741 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AVA [auth u]1,382Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107581 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EWA [auth v]445Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104408 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DYA [auth x]548Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100353 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CZA [auth y]913Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184110 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5AB [auth z]430Homo sapiensMutation(s): 0 
Gene Names: EIF5
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GTEx:  ENSG00000100664 
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Entity ID: 7
MoleculeChains LengthOrganismImage
mRNAG [auth 7]255Homo sapiens
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Entity ID: 10
MoleculeChains LengthOrganismImage
18S rRNAJ [auth A]1,869Homo sapiens
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Entity ID: 50
MoleculeChains LengthOrganismImage
Initiator Met-tRNA-iXA [auth w]75Homo sapiens
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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 
GE [auth Q],
LE [auth k]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
BB [auth A]
BC [auth A]
AC [auth A],
AD [auth A],
AE [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth V],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth f],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth i],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth i],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTCoot0.9.8.1

Structure Validation

View Full Validation Report

Currently 8PJ2 does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
German Research Foundation (DFG)GermanyLeibniz-Preis

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references