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- EMDB-2845: 40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lac... -

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Basic information

Entry
Database: EMDB / ID: EMD-2845
Title40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri
Map dataStructure of the Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
Sample
  • Sample: Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
  • Complex: 40S
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1A
  • Protein or peptide: eIF3a
  • Protein or peptide: eIF3b
  • Protein or peptide: eIF3c
  • Protein or peptide: eIF3g
  • Protein or peptide: eIF3i
  • Protein or peptide: eIF3j
KeywordseIF3 / translation initiation
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / 90S preribosome / translation regulator activity ...eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / multi-eIF complex / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / 90S preribosome / translation regulator activity / translation initiation factor binding / translation initiation factor activity / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / RNA binding / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / : ...Eukaryotic translation initiation factor SUI1 / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / : / eIF3a, PCI domain, TPR-like region / Eukaryotic translation initiation factor 3 subunit A / 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 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / 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. / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / : / Ribosomal protein S30 / Ribosomal protein S7e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 40S ribosomal protein S1/3, eukaryotes / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4C / ES31 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S3 / US4 / Small ribosomal subunit protein uS5 / eIF1 / US7 / US8 / US9 ...Eukaryotic translation initiation factor 4C / ES31 / Small ribosomal subunit protein uS2 / 40S ribosomal protein S3 / US4 / Small ribosomal subunit protein uS5 / eIF1 / US7 / US8 / US9 / ES28 / US10 / US11 / US13 / US14 / US15 / US17 / Rack1 / US19 / 40S ribosomal protein S8 / ES19 / 40S ribosomal protein S12 / ES17 / 40S ribosomal protein S4 / 40S ribosomal protein S30 / 40S ribosomal protein S6 / 40S ribosomal protein S21 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit C / 40S ribosomal protein S7 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S26 / 40S ribosomal protein S27 / ES10 / 40S ribosomal protein S25 / 40S ribosomal protein S24 / RPS23
Similarity search - Component
Biological speciesLachancea kluyveri (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.47 Å
AuthorsAylett CHS / Boehringer D / Erzberger JP / Schaefer T / Ban N
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure of a yeast 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex.
Authors: Christopher H S Aylett / Daniel Boehringer / Jan P Erzberger / Tanja Schaefer / Nenad Ban /
Abstract: Eukaryotic translation initiation requires cooperative assembly of a large protein complex at the 40S ribosomal subunit. We have resolved a budding yeast initiation complex by cryo-EM, allowing ...Eukaryotic translation initiation requires cooperative assembly of a large protein complex at the 40S ribosomal subunit. We have resolved a budding yeast initiation complex by cryo-EM, allowing placement of prior structures of eIF1, eIF1A, eIF3a, eIF3b and eIF3c. Our structure highlights differences in initiation-complex binding to the ribosome compared to that of mammalian eIF3, demonstrates a direct contact between eIF3j and eIF1A and reveals the network of interactions between eIF3 subunits.
History
DepositionDec 18, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseFeb 11, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4uer
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emdb-2845.png

Downloads & links

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Map

FileDownload / File: emd_2845.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.0193239 - 0.11476482
Average (Standard dev.)0.00174344 (±0.01196989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0190.1150.002

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Supplemental data

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Sample components

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Entire : Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex

EntireName: Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
Components
  • Sample: Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
  • Complex: 40S
  • Protein or peptide: eIF1
  • Protein or peptide: eIF1A
  • Protein or peptide: eIF3a
  • Protein or peptide: eIF3b
  • Protein or peptide: eIF3c
  • Protein or peptide: eIF3g
  • Protein or peptide: eIF3i
  • Protein or peptide: eIF3j

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Supramolecule #1000: Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex

SupramoleculeName: Lachancea kluyveri 40S-eIF1-eIF1A-eIF3-eIF3j initiation complex
type: sample / ID: 1000 / Number unique components: 9
Molecular weightTheoretical: 1.6 MDa

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Supramolecule #1: 40S

SupramoleculeName: 40S / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: SSU 40S
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: eIF1

MacromoleculeName: eIF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 10 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #2: eIF1A

MacromoleculeName: eIF1A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 20 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #3: eIF3a

MacromoleculeName: eIF3a / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 120 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #4: eIF3b

MacromoleculeName: eIF3b / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 90 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #5: eIF3c

MacromoleculeName: eIF3c / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 90 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #6: eIF3g

MacromoleculeName: eIF3g / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #7: eIF3i

MacromoleculeName: eIF3i / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 40 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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Macromolecule #8: eIF3j

MacromoleculeName: eIF3j / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Lachancea kluyveri (fungus) / Location in cell: Cytoplasmic
Molecular weightTheoretical: 30 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pLIC

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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

Concentration0.2 mg/mL
BufferpH: 7.6 / Details: 25 mM K-HEPES, 10 mM MgCl2, 75 mM KCl, 0.5 mM TCEP
GridDetails: 200 mesh Quantifoil R 2/2 holey carbon grids with a thin continuous carbon support film
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER
Details: carbon floated on the sample prior to recovery onto the grid and flash-freezing.
Method: 5 seconds blotting before plunging.

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateApr 6, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 7200 / Average electron dose: 25 e/Å2
Details: Single movie frame readout. 7 frames per exposure. 4 images per hole.
Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TITAN KRIOS
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateJul 16, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 8828 / Average electron dose: 25 e/Å2
Details: Single movie frame readout. 7 frames per exposure. Drift corrected in post-processing. 4 images per hole.
Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100719 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsFor full details see the supplemental materials and methods in the accompanying publication which provides processing details and the classification schema.
CTF correctionDetails: By image
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.47 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.2 / Number images used: 27354

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Atomic model buiding 1

Initial modelPDB ID:

3u5b
PDB Unreleased entry

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 2

Initial modelPDB ID:

3u5g
PDB Unreleased entry

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 3

Initial modelPDB ID:

4u1c

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 4

Initial modelPDB ID:

4u1d

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 5

Initial modelPDB ID:

4u1f

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 6

Initial modelPDB ID:

3ns6

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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Atomic model buiding 7

Initial modelPDB ID:

4bpp
PDB Unreleased entry

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation
Output model

PDB-4uer:
40S-eIF1-eIF1A-eIF3-eIF3j translation initiation complex from Lachancea kluyveri

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