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

  • 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0D [auth A]254Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1E [auth B]255Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWD0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F09812pF [auth C]259Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D08305pG [auth D]237Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CRK7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4H [auth E]261Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D10659pI [auth F]227Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]236Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth H]190Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth I]201Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E23673pM [auth J]188Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B08173pN [auth K]106Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CVZ5 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0A10483pO [auth L]156Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12P [auth M]134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F18040pQ [auth N]151Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14R [auth O]137Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P27069 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F07843pS [auth P]142Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16T [auth Q]143Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B01474pU [auth R]136Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWU3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B01562pV [auth S]146Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWT9 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0A07194pW [auth T]144Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CXM0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F25542pX [auth U]117Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CIM1 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Y [auth V]87Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S22Z [auth W]130Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B11231pAA [auth X]145Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24BA [auth Y]135Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B06182pCA [auth Z]108Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26DA [auth a]119Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27EA [auth b]82Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth c]67Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth d]56Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth e]63Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aIA [auth f]150Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for P69061 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E12277pJA [auth g]326Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AKA [auth h]25Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 1ALA [auth i]153Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF11YMR260CYM8156.02C
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaMA [auth j]304Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI2TIF211YJR007WJ1429
UniProt
Find proteins for P20459 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit gammaNA [auth k]527Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCD11TIF213YER025W
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit betaOA [auth l]285Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI3TIF212YPL237W
UniProt
Find proteins for P09064 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5PA [auth m]405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF5YPR041WYP3085.05
UniProt
Find proteins for P38431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit AQA [auth o]964Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPG1TIF32YBR079CYBR0734
UniProt
Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38249
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BRA [auth p]763Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRT1CDC63YOR361C
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eIF3c,eIF3cSA [auth q]812Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GTA [auth r]274Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF35SCY_1313
UniProt
Find proteins for A6ZZ25 (Saccharomyces cerevisiae (strain YJM789))
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UniProt GroupA6ZZ25
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit IUA [auth s]347Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF34YMR146CYM9375.16C
UniProt
Find proteins for P40217 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChains LengthOrganismImage
tRNAiA [auth 1]75Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
18S ribosomal RNAB [auth 2]1,798Kluyveromyces lactis NRRL Y-1140
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Entity ID: 3
MoleculeChains LengthOrganismImage
mRNA (31-MER)C [auth 3]49Saccharomyces cerevisiae
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

Download Ideal Coordinates CCD File 
MF [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
MET
Query on MET

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

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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],
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
Modified Residues  1 Unique
IDChains TypeFormula2D 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 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8

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