6FYX

Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain (model C1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Translational initiation factor eIF5 replaces eIF1 on the 40S ribosomal subunit to promote start-codon recognition.

Llacer, J.L.Hussain, T.Saini, A.K.Nanda, J.D.Kaur, S.Gordiyenko, Y.Kumar, R.Hinnebusch, A.G.Lorsch, J.R.Ramakrishnan, V.

(2018) Elife 7

  • DOI: 10.7554/eLife.39273
  • Primary Citation of Related Structures:  
    6FYY, 6FYX

  • PubMed Abstract: 
  • In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA i in a 'P IN ' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown ...

    In eukaryotic translation initiation, AUG recognition of the mRNA requires accommodation of Met-tRNA i in a 'P IN ' state, which is antagonized by the factor eIF1. eIF5 is a GTPase activating protein (GAP) of eIF2 that additionally promotes stringent AUG selection, but the molecular basis of its dual function was unknown. We present a cryo-electron microscopy (cryo-EM) reconstruction of a yeast 48S pre-initiation complex (PIC), at an overall resolution of 3.0 Å, featuring the N-terminal domain (NTD) of eIF5 bound to the 40S subunit at the location vacated by eIF1. eIF5 interacts with and allows a more accommodated orientation of Met-tRNA i . Substitutions of eIF5 residues involved in the eIF5-NTD/tRNA i interaction influenced initiation at near-cognate UUG codons in vivo, and the closed/open PIC conformation in vitro, consistent with direct stabilization of the codon:anticodon duplex by the wild-type eIF5-NTD. The present structure reveals the basis for a key role of eIF5 in start-codon selection.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0D [auth A]254Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS0KLLA0E16171g
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1E [auth B]255Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS1KLLA0B05060g
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F09812pF [auth C]259Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F09812g
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D08305pG [auth D]237Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_D08305g
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4H [auth E]261Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B03652g
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0D10659pI [auth F]227Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_D10659g
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Entity ID: 10
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40S ribosomal protein S6J [auth G]236Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS6KLLA0E24090g
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Entity ID: 11
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40S ribosomal protein S7K [auth H]190Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_C13519g
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Entity ID: 12
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40S ribosomal protein S8L [auth I]201Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E20461g
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Entity ID: 13
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KLLA0E23673pM [auth J]188Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E23673g
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B08173pN [auth K]106Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B08173g
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0A10483pO [auth L]156Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_A10483g
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Entity ID: 16
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40S ribosomal protein S12P [auth M]134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F00352g
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Entity ID: 17
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KLLA0F18040pQ [auth N]151Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F18040g
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S14R [auth O]137Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS14CRY1KLLA0B07623g
UniProt
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F07843pS [auth P]142Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F07843g
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Entity ID: 20
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40S ribosomal protein S16T [auth Q]143Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS16KLLA0E22077g
UniProt
Find proteins for Q875N2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B01474pU [auth R]136Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B01474g
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B01562pV [auth S]146Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B01562g
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0A07194pW [auth T]144Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_A07194g
UniProt
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0F25542pX [auth U]117Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_F25542g
UniProt
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S21Y [auth V]87Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS21KLLA0A05700g
UniProt
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S22Z [auth W]130Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS22KLLA0B07601g
UniProt
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B11231pAA [auth X]145Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B11231g
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S24BA [auth Y]135Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_C07755g
UniProt
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
KLLA0B06182pCA [auth Z]108Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_B06182g
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Entity ID: 30
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40S ribosomal protein S26DA [auth a]119Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_D05115g
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Entity ID: 31
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40S ribosomal protein S27EA [auth b]82Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E11661g
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Entity ID: 32
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40S ribosomal protein S28FA [auth c]67Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS28KLLA0F20383g
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Entity ID: 33
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40S ribosomal protein S29GA [auth d]56Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: RPS29KLLA0E05071g
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Entity ID: 34
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40S ribosomal protein S30HA [auth e]63Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_C04809g
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Entity ID: 35
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Ubiquitin-40S ribosomal protein S27aIA [auth f]150Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: ubi3KLLA0D18304g
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Entity ID: 36
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KLLA0E12277pJA [auth g]326Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
Gene Names: KLLA0_E12277g
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Entity ID: 37
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60S ribosomal protein L41-AKA [auth h]25Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 38
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Eukaryotic translation initiation factor 1ALA [auth i]153Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF11YMR260CYM8156.02C
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Entity ID: 39
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Eukaryotic translation initiation factor 2 subunit alphaMA [auth j]304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
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Entity ID: 40
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Eukaryotic translation initiation factor 2 subunit gammaNA [auth k]527Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCD11TIF213YER025WSUI4
EC: 3.6.5.3
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Entity ID: 41
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Eukaryotic translation initiation factor 2 subunit betaOA [auth l]285Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI3TIF212YPL237W
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Entity ID: 42
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Eukaryotic translation initiation factor 5PA [auth m]405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF5YPR041WYP3085.05
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Entity ID: 43
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Eukaryotic translation initiation factor 3 subunit AQA [auth o]964Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPG1TIF32YBR079CYBR0734
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Entity ID: 44
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Eukaryotic translation initiation factor 3 subunit BRA [auth p]763Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRT1CDC63YOR361C
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Entity ID: 45
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eIF3c,eIF3cSA [auth q]812Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NIP1
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Entity ID: 46
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Eukaryotic translation initiation factor 3 subunit GTA [auth r]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF35SCY_1313
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Find proteins for A6ZZ25 (Saccharomyces cerevisiae (strain YJM789))
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Entity ID: 47
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Eukaryotic translation initiation factor 3 subunit IUA [auth s]347Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF34YMR146CYM9375.16C
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Entity ID: 1
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tRNAiA [auth 1]75Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganismImage
18S ribosomal RNAB [auth 2]1798Kluyveromyces lactis NRRL Y-1140
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
mRNA (31-MER)C [auth 3]49Saccharomyces cerevisiae
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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MF [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
MET
Query on MET

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KF [auth k]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

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HF [auth a], IF [auth b], JF [auth f], NF [auth l], OF [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth 2] , AC [auth 2] , AD [auth 2] , AE [auth 2] , AF [auth 2] , BB [auth 2] , BC [auth 2] , BD [auth 2] , 
AB [auth 2],  AC [auth 2],  AD [auth 2],  AE [auth 2],  AF [auth 2],  BB [auth 2],  BC [auth 2],  BD [auth 2],  BE [auth 2],  BF [auth 2],  CB [auth 2],  CC [auth 2],  CD [auth 2],  CE [auth 2],  CF [auth 2],  DB [auth 2],  DC [auth 2],  DD [auth 2],  DE [auth 2],  DF [auth 2],  EB [auth 2],  EC [auth 2],  ED [auth 2],  EE [auth 2],  EF [auth 2],  FB [auth 2],  FC [auth 2],  FD [auth 2],  FE [auth 2],  FF [auth 2],  GB [auth 2],  GC [auth 2],  GD [auth 2],  GE [auth 2],  GF [auth 2],  HB [auth 2],  HC [auth 2],  HD [auth 2],  HE [auth 2],  IB [auth 2],  IC [auth 2],  ID [auth 2],  IE [auth 2],  JB [auth 2],  JC [auth 2],  JD [auth 2],  JE [auth 2],  KB [auth 2],  KC [auth 2],  KD [auth 2],  KE [auth 2],  LB [auth 2],  LC [auth 2],  LD [auth 2],  LE [auth 2],  LF [auth k],  MB [auth 2],  MC [auth 2],  MD [auth 2],  ME [auth 2],  NB [auth 2],  NC [auth 2],  ND [auth 2],  NE [auth 2],  OB [auth 2],  OC [auth 2],  OD [auth 2],  OE [auth 2],  PB [auth 2],  PC [auth 2],  PD [auth 2],  PE [auth 2],  QB [auth 2],  QC [auth 2],  QD [auth 2],  QE [auth 2],  RB [auth 2],  RC [auth 2],  RD [auth 2],  RE [auth 2],  SB [auth 2],  SC [auth 2],  SD [auth 2],  SE [auth 2],  TB [auth 2],  TC [auth 2],  TD [auth 2],  TE [auth 2],  UB [auth 2],  UC [auth 2],  UD [auth 2],  UE [auth 2],  VA [auth 2],  VB [auth 2],  VC [auth 2],  VD [auth 2],  VE [auth 2],  WA [auth 2],  WB [auth 2],  WC [auth 2],  WD [auth 2],  WE [auth 2],  XA [auth 2],  XB [auth 2],  XC [auth 2],  XD [auth 2],  XE [auth 2],  YA [auth 2],  YB [auth 2],  YC [auth 2],  YD [auth 2],  YE [auth 2],  ZA [auth 2],  ZB [auth 2],  ZC [auth 2],  ZD [auth 2],  ZE [auth 2]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AYA
Query on AYA
E [auth B]L-PEPTIDE LINKINGC5 H9 N O3ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMC_U105184332
Wellcome TrustUnited KingdomWT096570
FEBSUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Other