6YBW

Structure of a human 48S translational initiation complex - 40S body


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

Structure of a human 48Stranslational initiation complex.

Brito Querido, J.Sokabe, M.Kraatz, S.Gordiyenko, Y.Skehel, J.M.Fraser, C.S.Ramakrishnan, V.

(2020) Science 369: 1220-1227

  • DOI: https://doi.org/10.1126/science.aba4904
  • Primary Citation of Related Structures:  
    6YBD, 6YBS, 6YBT, 6YBV, 6YBW, 6ZMW

  • PubMed Abstract: 

    A key step in translational initiation is the recruitment of the 43 S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 S initiation complex (i.e., the 48 S ). The 48 S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 S The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 S The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 S subunit during scanning.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformA [auth C]263Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198034 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11157Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142534 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23C [auth E]143Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000186468 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170889 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7E [auth G]194Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171863 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3059Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149806 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27G [auth H]84Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177954 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21H [auth K]83Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000171858 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aI [auth J]130Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134419 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17J [auth M]135Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000182774 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2K [auth L]293Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000140988 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aL [auth O]264Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145425 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAM [auth N]295Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168028 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26N [auth Q]115Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197728 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14O [auth P]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164587 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6P [auth S]249Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000137154 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8Q [auth R]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000142937 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24R [auth T]133Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138326 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1A, X-chromosomalS [auth q]144Homo sapiensMutation(s): 0 
Gene Names: EIF1AXEIF1AEIF4C
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GTEx:  ENSG00000173674 
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UniProt GroupP47813
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1T [auth p]113Homo sapiensMutation(s): 0 
Gene Names: EIF1SUI1
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GTEx:  ENSG00000173812 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13U [auth I]151Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110700 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit JV [auth z]258Homo sapiensMutation(s): 0 
Gene Names: EIF3JEIF3S1PRO0391
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GTEx:  ENSG00000104131 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CW [auth y]913Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000184110 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41X [auth 9]25Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000229117 
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Entity ID: 25
MoleculeChains LengthOrganismImage
18S rRNAY [auth A]1,869Homo sapiens
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Entity ID: 26
MoleculeChains LengthOrganismImage
mRNAZ [auth 7]28Homo sapiens
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
BA [auth Q]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AA [auth L]
AB [auth A]
AC [auth A]
BB [auth A]
BC [auth A]
AA [auth L],
AB [auth A],
AC [auth A],
BB [auth A],
BC [auth A],
CA [auth S],
CB [auth A],
CC [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
JA [auth A],
JB [auth A],
KA [auth A],
KB [auth A],
LA [auth A],
LB [auth A],
MA [auth A],
MB [auth A],
NA [auth A],
NB [auth A],
OA [auth A],
OB [auth A],
PA [auth A],
PB [auth A],
QA [auth A],
QB [auth A],
RA [auth A],
RB [auth A],
SA [auth A],
SB [auth A],
TA [auth A],
TB [auth A],
UA [auth A],
UB [auth A],
VA [auth A],
VB [auth A],
WA [auth A],
WB [auth A],
XA [auth A],
XB [auth A],
YA [auth A],
YB [auth A],
ZA [auth A],
ZB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited KingdomWTY096570
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184332
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM092927

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection, Database references