6GSN image
Deposition Date 2018-06-14
Release Date 2019-06-26
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6GSN
Keywords:
Title:
Structure of a partial yeast 48S preinitiation complex in closed conformation
Biological Source:
Method Details:
Experimental Method:
Resolution:
5.75 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:tRNAi (75-MER)
Chain IDs:BA (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polyribonucleotide
Molecule:18S rRNA (1798-MER)
Chain IDs:A (auth: 2)
Chain Length:1798
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:T (auth: 3)
Chain Length:14
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0
Gene (Uniprot):RPS0
Chain IDs:CA (auth: A)
Chain Length:219
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1
Gene (Uniprot):RPS1
Chain IDs:DA (auth: B)
Chain Length:231
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0F09812p
Gene (Uniprot):KLLA0_F09812g
Chain IDs:B (auth: C)
Chain Length:62
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0D08305p
Gene (Uniprot):KLLA0_D08305g
Chain IDs:C (auth: D)
Chain Length:53
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4
Gene (Uniprot):KLLA0_B03652g
Chain IDs:EA (auth: E)
Chain Length:58
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0D10659p
Gene (Uniprot):KLLA0_D10659g
Chain IDs:D (auth: F)
Chain Length:69
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6
Gene (Uniprot):RPS6
Chain IDs:FA (auth: G)
Chain Length:324
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7
Gene (Uniprot):KLLA0_C13519g
Chain IDs:GA (auth: H)
Chain Length:25
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8
Gene (Uniprot):KLLA0_E20461g
Chain IDs:HA (auth: I)
Chain Length:200
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0E23673p
Gene (Uniprot):KLLA0_E23673g
Chain IDs:IA (auth: J)
Chain Length:182
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0B08173p
Gene (Uniprot):KLLA0_B08173g
Chain IDs:E (auth: K)
Chain Length:430
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0A10483p
Gene (Uniprot):KLLA0_A10483g
Chain IDs:JA (auth: L)
Chain Length:144
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S12
Gene (Uniprot):KLLA0_F00352g
Chain IDs:F (auth: M)
Chain Length:90
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0F18040p
Gene (Uniprot):KLLA0_F18040g
Chain IDs:KA (auth: N)
Chain Length:150
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14
Gene (Uniprot):RPS14
Chain IDs:LA (auth: O)
Chain Length:127
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0F07843p
Gene (Uniprot):KLLA0_F07843g
Chain IDs:G (auth: P)
Chain Length:117
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16
Gene (Uniprot):RPS16
Chain IDs:H (auth: Q)
Chain Length:141
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0B01474p
Gene (Uniprot):KLLA0_B01474g
Chain IDs:I (auth: R)
Chain Length:130
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0B01562p
Gene (Uniprot):KLLA0_B01562g
Chain IDs:J (auth: S)
Chain Length:342
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0A07194p
Gene (Uniprot):KLLA0_A07194g
Chain IDs:K (auth: T)
Chain Length:143
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0F25542p
Gene (Uniprot):KLLA0_F25542g
Chain IDs:L (auth: U)
Chain Length:106
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21
Gene (Uniprot):RPS21
Chain IDs:MA (auth: V)
Chain Length:87
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22
Gene (Uniprot):RPS22
Chain IDs:NA (auth: W)
Chain Length:129
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:RPS23
Chain IDs:PA (auth: X)
Chain Length:144
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24
Gene (Uniprot):KLLA0_C07755g
Chain IDs:OA (auth: Y)
Chain Length:134
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0B06182p
Gene (Uniprot):KLLA0_B06182g
Chain IDs:M (auth: Z)
Chain Length:70
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26
Gene (Uniprot):KLLA0_D05115g
Chain IDs:QA (auth: a)
Chain Length:219
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27
Gene (Uniprot):KLLA0_E11661g
Chain IDs:RA (auth: b)
Chain Length:231
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28
Gene (Uniprot):RPS28
Chain IDs:N (auth: c)
Chain Length:62
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29
Gene (Uniprot):RPS29
Chain IDs:Q (auth: d)
Chain Length:53
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30
Gene (Uniprot):KLLA0_C04809g
Chain IDs:R (auth: e)
Chain Length:58
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S27a
Gene (Uniprot):ubi3
Chain IDs:O (auth: f)
Chain Length:69
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:KLLA0E12277p
Gene (Uniprot):KLLA0_E12277g
Chain IDs:P (auth: g)
Chain Length:324
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:S (auth: h)
Chain Length:25
Number of Molecules:1
Biological Source:Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 1A
Gene (Uniprot):TIF11
Chain IDs:U (auth: i)
Chain Length:200
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit alpha
Gene (Uniprot):SUI2
Chain IDs:AA (auth: j)
Chain Length:182
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit gamma
Gene (Uniprot):GCD11
Chain IDs:Y (auth: k)
Chain Length:430
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 2 subunit beta
Gene (Uniprot):SUI3
Chain IDs:Z (auth: l)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor eIF-1
Gene (Uniprot):SUI1
Chain IDs:V (auth: m)
Chain Length:90
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit A,eIF3a
Gene (Uniprot):RPG1
Chain IDs:W (auth: o)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit B
Gene (Uniprot):PRT1
Chain IDs:SA (auth: p)
Chain Length:117
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit C
Gene (Uniprot):NIP1
Chain IDs:X (auth: q)
Chain Length:141
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit G
Gene (Uniprot):TIF35
Chain IDs:UA (auth: r)
Chain Length:130
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 3 subunit I
Chain IDs:TA (auth: s)
Chain Length:342
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Primary Citation
Large-scale movement of eIF3 domains during translation initiation modulate start codon selection.
Nucleic Acids Res. ? ? ? (2021)
PMID: 34648019 DOI: 10.1093/nar/gkab908

Abstact

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.

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Primary Citation of related structures