6GSM

Structure of a partial yeast 48S preinitiation complex in open conformation.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Large-scale movement of eIF3 domains during translation initiation modulate start codon selection.

Llacer, J.L.Hussain, T.Dong, J.Villamayor, L.Gordiyenko, Y.Hinnebusch, A.G.

(2021) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkab908
  • Primary Citation of Related Structures:  
    6GSM, 6GSN

  • PubMed Abstract: 

    The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia 46010, Spain.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S0C [auth A]208Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S1E [auth B]231Kluyveromyces 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]217Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D08305pG [auth D]223Kluyveromyces 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]260Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CWJ2 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0D10659pI [auth F]206Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Find proteins for Q6CRA3 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6J [auth G]226Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CM04 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7K [auth H]184Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CTD6 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8L [auth I]200Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0E23673pM [auth J]182Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Find proteins for Q6CM18 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B08173pN [auth K]96Kluyveromyces 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]155Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Find proteins for Q6CX80 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12P [auth M]118Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CLU4 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0F18040pQ [auth N]150Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CJK0 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14R [auth O]127Kluyveromyces 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]119Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S16T [auth Q]141Kluyveromyces 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]125Kluyveromyces 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]145Kluyveromyces 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]143Kluyveromyces 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]106Kluyveromyces 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]129Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B11231pAA [auth X]144Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24BA [auth Y]134Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
KLLA0B06182pCA [auth Z]70Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26DA [auth a]98Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27EA [auth b]81Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28FA [auth c]62Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29GA [auth d]53Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30HA [auth e]58Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27aIA [auth f]69Kluyveromyces 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]324Kluyveromyces lactis NRRL Y-1140Mutation(s): 0 
UniProt
Find proteins for Q6CNI7 (Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37))
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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]95Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF11YMR260CYM8156.02C
UniProt
Find proteins for P38912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit alphaMA [auth j]263Saccharomyces 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]430Saccharomyces 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]144Saccharomyces 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 eIF-1PA [auth m]96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUI1RFR1YNL244CN0905
UniProt
Find proteins for P32911 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32911
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit A,Eukaryotic translation initiation factor 3 subunit A,eIF3aQA [auth o]567Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPG1TIF32YBR079CYBR0734
UniProt
Find proteins for P38249 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit BRA [auth p]651Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRT1CDC63YOR361C
UniProt
Find proteins for P06103 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit CSA [auth q]665Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NIP1YMR309CYM9924.01CYM9952.11C
UniProt
Find proteins for P32497 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit ITA [auth s]342Saccharomyces 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: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit GUA [auth r]49Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TIF35YDR429CD9461.16
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
Met-tRNAiA [auth 1]76Saccharomyces cerevisiae S288C
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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: 4
MoleculeChains LengthOrganismImage
mRNA (5'-R(P*AP*AP*U)-3')D [auth 3]3Kluyveromyces lactis
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP
Query on GCP

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DE [auth k]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
7NO
Query on 7NO

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VA [auth 1][(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-2-(phosphonooxymethyl)oxolan-3-yl] (2~{S})-2-azanyl-4-methylsulfanyl-butanoate
C15 H23 N6 O8 P S
QTJGZHBCXHRMIV-TWBCTODHSA-N
ZN
Query on ZN

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AE [auth b],
BE [auth f],
EE [auth l],
YD [auth O]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 2]
AC [auth 2]
AD [auth 2]
BB [auth 2]
BC [auth 2]
AB [auth 2],
AC [auth 2],
AD [auth 2],
BB [auth 2],
BC [auth 2],
BD [auth 2],
CB [auth 2],
CC [auth 2],
CD [auth 2],
CE [auth k],
DB [auth 2],
DC [auth 2],
DD [auth 2],
EB [auth 2],
EC [auth 2],
ED [auth 2],
FB [auth 2],
FC [auth 2],
FD [auth 2],
GB [auth 2],
GC [auth 2],
GD [auth 2],
HB [auth 2],
HC [auth 2],
HD [auth 2],
IB [auth 2],
IC [auth 2],
ID [auth 2],
JB [auth 2],
JC [auth 2],
JD [auth 2],
KB [auth 2],
KC [auth 2],
KD [auth 2],
LB [auth 2],
LC [auth 2],
LD [auth 2],
MB [auth 2],
MC [auth 2],
MD [auth 2],
NB [auth 2],
NC [auth 2],
ND [auth 2],
OB [auth 2],
OC [auth 2],
OD [auth 2],
PB [auth 2],
PC [auth 2],
PD [auth 2],
QB [auth 2],
QC [auth 2],
QD [auth 2],
RB [auth 2],
RC [auth 2],
RD [auth 2],
SB [auth 2],
SC [auth 2],
SD [auth 2],
TB [auth 2],
TC [auth 2],
TD [auth 2],
UB [auth 2],
UC [auth 2],
UD [auth C],
VB [auth 2],
VC [auth 2],
VD [auth C],
WA [auth 2],
WB [auth 2],
WC [auth 2],
WD [auth C],
XA [auth 2],
XB [auth 2],
XC [auth 2],
XD [auth O],
YA [auth 2],
YB [auth 2],
YC [auth 2],
ZA [auth 2],
ZB [auth 2],
ZC [auth 2],
ZD [auth Q]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.15 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
Wellcome TrustUnited KingdomWT096570

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2021-08-25
    Type: Coordinate replacement
    Changes: Advisory, Database references, Derived calculations
  • Version 1.2: 2021-10-27
    Changes: Data collection, Database references
  • Version 2.0: 2022-07-20
    Type: Coordinate replacement
    Reason: Polymer geometry
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-02-22
    Changes: Structure summary