- EMDB-35216: Yeast 40S-eIF4B - partially open conformation of the 40S head -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-35216
Title
Yeast 40S-eIF4B - partially open conformation of the 40S head
Map data
This is the cryo-EM map of the 40S-eIF4B complex from yeast.
Sample
Complex: The binary complex of the yeast 40S small ribosomal subunit with the eukaryotic initiation factor 4B.
Complex: Eukaryotic Initiation Factor 4B (eIF4B).
Protein or peptide: x 1 types
Complex: yeast 40S small ribosomal subunit
RNA: x 1 types
Protein or peptide: x 33 types
Ligand: x 2 types
Keywords
RIBOSOME
Function / homology
Function and homology information
endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / translation regulator activity / 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) / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding ...endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / translation regulator activity / 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) / rescue of stalled ribosome / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / protein kinase C binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / 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 / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function
: / Ribosomal protein S26e signature. / : / 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 S26e signature. / : / 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 S21e / Ribosomal protein S2, eukaryotic / Ribosomal protein S21e superfamily / Ribosomal protein S21e / S27a-like superfamily / 40S Ribosomal protein S10 / Ribosomal protein S10, eukaryotic/archaeal / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / : / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / 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 / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S24e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S24e / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S27 / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / Ribosomal protein S28e signature. / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e / Ribosomal protein S28e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e Similarity search - Domain/homology
KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / KLLA0F25542p / KLLA0F18040p / KLLA0F09812p / KLLA0F07843p / 40S ribosomal protein S12 ...KLLA0B11231p / Small ribosomal subunit protein eS32A / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein eS28 / Ubiquitin-ribosomal protein eS31 fusion protein / 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 / KLLA0B07931p / 40S ribosomal protein S25 / Small ribosomal subunit protein eS1 / 40S ribosomal protein S4 / KLLA0B01562p / KLLA0B01474p / KLLA0A10483p / KLLA0A07194p / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein uS9 Similarity search - Component
Entire : The binary complex of the yeast 40S small ribosomal subunit with ...
Entire
Name: The binary complex of the yeast 40S small ribosomal subunit with the eukaryotic initiation factor 4B.
Components
Complex: The binary complex of the yeast 40S small ribosomal subunit with the eukaryotic initiation factor 4B.
Complex: Eukaryotic Initiation Factor 4B (eIF4B).
Protein or peptide: 60S ribosomal protein L41-A
Complex: yeast 40S small ribosomal subunit
RNA: RNA (1780-MER)
Protein or peptide: 40S ribosomal protein S0
Protein or peptide: 40S ribosomal protein S1
Protein or peptide: KLLA0F09812p
Protein or peptide: KLLA0D08305p
Protein or peptide: 40S ribosomal protein S4
Protein or peptide: KLLA0D10659p
Protein or peptide: 40S ribosomal protein S6
Protein or peptide: 40S ribosomal protein S7
Protein or peptide: 40S ribosomal protein S8
Protein or peptide: KLLA0E23673p
Protein or peptide: KLLA0B08173p
Protein or peptide: KLLA0A10483p
Protein or peptide: 40S ribosomal protein S12
Protein or peptide: KLLA0F18040p
Protein or peptide: 40S ribosomal protein S14
Protein or peptide: KLLA0F07843p
Protein or peptide: 40S ribosomal protein S16
Protein or peptide: KLLA0B01474p
Protein or peptide: KLLA0B01562p
Protein or peptide: KLLA0A07194p
Protein or peptide: KLLA0F25542p
Protein or peptide: 40S ribosomal protein S21
Protein or peptide: KLLA0B07931p
Protein or peptide: KLLA0B11231p
Protein or peptide: 40S ribosomal protein S24
Protein or peptide: 40S ribosomal protein S25
Protein or peptide: 40S ribosomal protein S26
Protein or peptide: 40S ribosomal protein S27
Protein or peptide: 40S ribosomal protein S28
Protein or peptide: 40S ribosomal protein S29
Protein or peptide: 40S ribosomal protein S30
Protein or peptide: Ubiquitin-40S ribosomal protein S27a
Protein or peptide: KLLA0E12277p
Ligand: MAGNESIUM ION
Ligand: ZINC ION
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Supramolecule #1: The binary complex of the yeast 40S small ribosomal subunit with ...
Supramolecule
Name: The binary complex of the yeast 40S small ribosomal subunit with the eukaryotic initiation factor 4B. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35 Details: 40S purified from Kluyveromyces lactis and Saccharomyces cerevisiae eIF4B overexpressed and purified from Escherichia coli
Source (natural)
Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Tissue: Single cell yeast / Location in cell: cytoplasm
Name: Eukaryotic Initiation Factor 4B (eIF4B). / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #35 Details: eIF4B is a part of the binary complex along with the 40S ribosomal subunit. eIF4B is present and associated with the 40S near its mRNA channel entry site on the solvent-exposed side. The ...Details: eIF4B is a part of the binary complex along with the 40S ribosomal subunit. eIF4B is present and associated with the 40S near its mRNA channel entry site on the solvent-exposed side. The Saccharomyces cerevisiae eIF4B was recombinantly expressed and purified from the E. coli expression system.
Name: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 2 / Formula: MG
Molecular weight
Theoretical: 24.305 Da
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Macromolecule #37: ZINC ION
Macromolecule
Name: ZINC ION / type: ligand / ID: 37 / Number of copies: 3 / Formula: ZN
Molecular weight
Theoretical: 65.409 Da
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.4 Component:
Concentration
Formula
Name
20.0 mM
C8H18N2O4S
HEPES
100.0 mM
CH3CO2K
Potassium acetate
2.5 mM
C2H6O4Mg
Magnesium acetate
2.0 mM
C4H10O2S2
Dithiothreitol
Details: 20 mM HEPES pH7.4, 100 mM potassium acetate pH7.6, 2.5 mM Magnesium acetate, 2 mM DTT
Grid
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Vitrification was carried out in nitrogen atmosphere..
Details
This class of empty or only 40S was a part of the reaction mixture containing 40S and the Saccharomyces cerevisiae eukaryotic initiation factor 4B present in a 1:10 molar ratio
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Electron microscopy
Microscope
FEI TALOS ARCTICA
Temperature
Min: 77.0 K / Max: 98.0 K
Details
Preliminary grid screening was done manually using the Latitude-S
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 4-16 / Number grids imaged: 6 / Number real images: 7975 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 Details: Images were collected in movie-mode at 20 frames in 8 seconds
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
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