8PJ5

Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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 5BA [auth 0]1,220Homo sapiensMutation(s): 0 
Gene Names: EIF5BIF2KIAA0741
EC: 3.6.5.3
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GTEx:  ENSG00000158417 
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UniProt GroupO60841
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BB [auth 1]814Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000106263 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IC [auth 2]325Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000084623 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit KD [auth 3]218Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000178982 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit FE [auth 4]357Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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GTEx:  ENSG00000175390 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit LF [auth 5]564Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100129 
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UniProt GroupQ9Y262
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit MG [auth 6]374Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149100 
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UniProt GroupQ7L2H7
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit HI [auth 8]352Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147677 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41J [auth 9]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11L [auth B]158Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformM [auth C]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9N [auth D]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23O [auth E]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30P [auth F]59Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7Q [auth G]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27R [auth H]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13S [auth I]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aT [auth J]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21U [auth K]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2V [auth L]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17W [auth M]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAX [auth N]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aY [auth O]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14Z [auth P]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26AA [auth Q]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8BA [auth R]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6CA [auth S]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24DA [auth T]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S5EA [auth V]204Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000083845 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16FA [auth Y]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105193 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3GA [auth Z]243Homo sapiensMutation(s): 0 
EC: 4.2.99.18
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GTEx:  ENSG00000149273 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10HA [auth a]165Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124614 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15IA [auth b]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000115268 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1JA [auth c]317Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19KA [auth d]145Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105372 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25LA [auth e]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118181 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18MA [auth f]152Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000231500 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20NA [auth h]119Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008988 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29OA [auth i]56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213741 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinPA [auth k]156Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143947 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12QA [auth m]132Homo sapiensMutation(s): 0 
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PHAROS:  P25398
GTEx:  ENSG00000112306 
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UniProt GroupP25398
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28RA [auth n]69Homo sapiensMutation(s): 0 
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PHAROS:  P62857
GTEx:  ENSG00000233927 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GSA [auth o]320Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130811 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1A, X-chromosomalTA [auth q]144Homo sapiensMutation(s): 0 
Gene Names: EIF1AXEIF1AEIF4C
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Find proteins for P47813 (Homo sapiens)
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PHAROS:  P47813
GTEx:  ENSG00000173674 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AUA [auth u]1,382Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000107581 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit EVA [auth v]445Homo sapiensMutation(s): 0 
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Find proteins for P60228 (Homo sapiens)
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GTEx:  ENSG00000104408 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit DXA [auth x]548Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100353 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CYA [auth y]913Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184110 
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Entity ID: 8
MoleculeChains LengthOrganismImage
mRNAH [auth 7]255Homo sapiens
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Entity ID: 11
MoleculeChains LengthOrganismImage
18S rRNAK [auth A]1,869Homo sapiens
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Entity ID: 49
MoleculeChains LengthOrganismImage
Initiator Met-tRNA-iWA [auth w]75Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AB [auth 0]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
LE [auth Q],
OE [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],
GE [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth P],
LB [auth A],
LC [auth A],
LD [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth S],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth f],
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],
ZA [auth 0],
ZB [auth A],
ZC [auth A],
ZD [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTCoot0.9.8.1

Structure Validation

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Currently 8PJ5 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