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- EMDB-3049: Structure of a partial yeast 48S preinitiation complex in open co... -

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Basic information

Entry
Database: EMDB / ID: EMD-3049
TitleStructure of a partial yeast 48S preinitiation complex in open conformation
Map dataTo see a continuous density for factor eIF3 at the 40S subunit interface, apply a Gaussian filtering of 1.8 and a contour level of 0.018.
Sample
  • Sample: Partial yeast 48S preinitiation complex in open conformation
  • Complex: Ribosome small subunit
  • Protein or peptide: Eukaryotic initiation factor 1
  • Protein or peptide: Eukaryotic initiation factor 1A
  • Protein or peptide: Eukaryotic initiation factor 2
  • Protein or peptide: Eukaryotic initiation factor 3
  • RNA: Initiator transfer RNA
  • RNA: Messenger RNA
KeywordsEukaryotic translation initiation / 48S / small ribosome subunit.
Function / homology
Function and homology information


formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site ...formation of translation initiation ternary complex / Cellular response to mitochondrial stress / Recycling of eIF2:GDP / eukaryotic translation initiation factor 3 complex, eIF3e / ABC-family proteins mediated transport / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 2 complex / incipient cellular bud site / multi-eIF complex / eukaryotic translation initiation factor 3 complex / selenocysteine metabolic process / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / positive regulation of translational fidelity / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation regulator activity / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translation initiation factor binding / translational initiation / translation initiation factor activity / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / double-stranded RNA binding / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / protein kinase binding / RNA binding / zinc ion binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / SUI1 domain superfamily / Translation initiation factor SUI1 ...Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit A / SUI1 domain / Eukaryotic translation initiation factor eIF2A / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / : / Ribosomal protein S26e signature. / S1 domain profile. / : / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S12e signature. / Ribosomal protein S12e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / 40S Ribosomal protein S10 / S27a-like superfamily / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S30 / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S7e signature. / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S19e / Ribosomal protein S3Ae signature. / Ribosomal_S19e / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S17e
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta / Small ribosomal subunit protein eS32A / Eukaryotic translation initiation factor 2 subunit alpha / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit gamma / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor eIF-1 ...Eukaryotic translation initiation factor 3 subunit G / KLLA0B11231p / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 2 subunit beta / Small ribosomal subunit protein eS32A / Eukaryotic translation initiation factor 2 subunit alpha / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit gamma / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor eIF-1 / Small ribosomal subunit protein eS28 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 1A / Eukaryotic translation initiation factor 3 subunit I / Ubiquitin-ribosomal protein eS31 fusion protein / Eukaryotic translation initiation factor 3 subunit G / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 / Small ribosomal subunit protein eS6 / KLLA0E23673p / 40S ribosomal protein S8 / Small ribosomal subunit protein uS2 / KLLA0E12277p / 40S ribosomal protein S27 / Small ribosomal subunit protein uS14 / KLLA0D10659p / 40S ribosomal protein S3 / 40S ribosomal protein S26 / 40S ribosomal protein S7 / 40S ribosomal protein S24 / 40S ribosomal protein S30 / KLLA0B08173p / Small ribosomal subunit protein uS8 / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / RPS23 / Small ribosomal subunit protein uS9
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsLlacer JL / Hussain T / Ramakrishnan V
CitationJournal: Mol Cell / Year: 2015
Title: Conformational Differences between Open and Closed States of the Eukaryotic Translation Initiation Complex.
Authors: Jose L Llácer / Tanweer Hussain / Laura Marler / Colin Echeverría Aitken / Anil Thakur / Jon R Lorsch / Alan G Hinnebusch / V Ramakrishnan /
Abstract: Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and ...Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2β as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.
History
DepositionJun 16, 2015-
Header (metadata) releaseJul 15, 2015-
Map releaseAug 5, 2015-
UpdateAug 19, 2015-
Current statusAug 19, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jaq
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6gsm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3049.png

emd_3049.png

Downloads & links

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Map

FileDownload / File: emd_3049.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTo see a continuous density for factor eIF3 at the 40S subunit interface, apply a Gaussian filtering of 1.8 and a contour level of 0.018.
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.05
Minimum - Maximum-0.08910795 - 0.20705962
Average (Standard dev.)0.00007748 (±0.0148471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 402.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z402.000402.000402.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0890.2070.000

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Supplemental data

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Supplemental map: p48S Pout half1 class001 unfil.map

Filep48S_Pout_half1_class001_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: p48S Pout half2 class001 unfil.map

Filep48S_Pout_half2_class001_unfil.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Partial yeast 48S preinitiation complex in open conformation

EntireName: Partial yeast 48S preinitiation complex in open conformation
Components
  • Sample: Partial yeast 48S preinitiation complex in open conformation
  • Complex: Ribosome small subunit
  • Protein or peptide: Eukaryotic initiation factor 1
  • Protein or peptide: Eukaryotic initiation factor 1A
  • Protein or peptide: Eukaryotic initiation factor 2
  • Protein or peptide: Eukaryotic initiation factor 3
  • RNA: Initiator transfer RNA
  • RNA: Messenger RNA

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Supramolecule #1000: Partial yeast 48S preinitiation complex in open conformation

SupramoleculeName: Partial yeast 48S preinitiation complex in open conformation
type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 7
Molecular weightTheoretical: 1.75 MDa

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Supramolecule #1: Ribosome small subunit

SupramoleculeName: Ribosome small subunit / type: complex / ID: 1 / Name.synonym: 40S / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S, SSU RNA 18S
Source (natural)Organism: Kluyveromyces lactis (yeast)
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Eukaryotic initiation factor 1

MacromoleculeName: Eukaryotic initiation factor 1 / type: protein_or_peptide / ID: 1 / Name.synonym: eIF1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 12.3 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta / Recombinant plasmid: pTYB2
SequenceUniProtKB: Eukaryotic translation initiation factor eIF-1

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Macromolecule #2: Eukaryotic initiation factor 1A

MacromoleculeName: Eukaryotic initiation factor 1A / type: protein_or_peptide / ID: 2 / Name.synonym: eIF1A / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: baker's yeast
Molecular weightTheoretical: 17.4 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta / Recombinant plasmid: pTYB2
SequenceUniProtKB: Eukaryotic translation initiation factor 1A

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Macromolecule #3: Eukaryotic initiation factor 2

MacromoleculeName: Eukaryotic initiation factor 2 / type: protein_or_peptide / ID: 3 / Name.synonym: eIF2
Details: Uniprot codes are: alpha-P20459 beta-P09064 gamma-P32481
Number of copies: 1 / Oligomeric state: Three subunits, alpha, beta, gamma / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 124 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant strain: GP3511

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Macromolecule #4: Eukaryotic initiation factor 3

MacromoleculeName: Eukaryotic initiation factor 3 / type: protein_or_peptide / ID: 4 / Name.synonym: eIF3
Details: Uniprot codes are: 3a-P38249, 3b-P06103, 3c-P32497, 3g-A6ZZ25, 3i-P40217
Number of copies: 1 / Oligomeric state: Five subunits, 3a, 3b, 3c, 3g, 3i / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 395 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta / Recombinant plasmid: pCDFDuet and pQlinkN

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Macromolecule #5: Initiator transfer RNA

MacromoleculeName: Initiator transfer RNA / type: rna / ID: 5 / Name.synonym: Met-tRNAi / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 23 KDa
SequenceString:
AGCGCCGUGG CGCAGUGGAA GCGCGCAGGG CUCAUAACCC UGAUGUCCUC GGAUCGAAAC CGAGCGGCGC UACCA

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Macromolecule #6: Messenger RNA

MacromoleculeName: Messenger RNA / type: rna / ID: 6 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.33 KDa
SequenceString:
GGAAUCUCUC UCUAUCCUCU CUCUC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.17 mg/mL
BufferpH: 6.5
Details: 20mM MES-KOH, 40mM K-acetate, 10mM NH4-acetate, 8mM Mg-acetate, 2mM DTT
GridDetails: Quantifoil R2/2 400 mesh copper grids with 4-5 nm thin carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I / Timed resolved state: 30 second incubation time / Method: Blot for 2.5-3 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 59,000 times magnification
DetailsComplete dataset was collected in 2 non-consecutive sessions
DateApr 28, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 2056 / Average electron dose: 27 e/Å2
Details: Complete dataset was collected in 2 non-consecutive sessions
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsParticles were automatically picked with the autopicking tool of Relion
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 4547
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j81


Chain - Chain ID: 2
SoftwareName: Chimera, Coot, Refmac
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: R-factor, FSC
Output model

PDB-6gsm:
Structure of a partial yeast 48S preinitiation complex in open conformation.

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Atomic model buiding 2

Initial modelPDB ID:

3cw2


Chain - Chain ID: K
SoftwareName: Chimera, Coot, Refmac
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: R-factor, FSC
Output model

PDB-6gsm:
Structure of a partial yeast 48S preinitiation complex in open conformation.

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Atomic model buiding 3

Initial modelPDB ID:

4u1d


Chain - Chain ID: A
SoftwareName: Chimera, Coot, Refmac
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: R-factor, FSC
Output model

PDB-6gsm:
Structure of a partial yeast 48S preinitiation complex in open conformation.

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