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- EMDB-2598: Cryo-EM of a termination/pre-recycling complex with eRF1 and ABCE1 -

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Basic information

Entry
Database: EMDB / ID: EMD-2598
TitleCryo-EM of a termination/pre-recycling complex with eRF1 and ABCE1
Map data"CMV-stalled" wheat germ 80S-RNC bound to eRF1 and ABCE1.
Sample
  • Sample: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
  • Complex: 80S ribosome
  • Protein or peptide: Sup45
  • Protein or peptide: Rli1
Keywordstranslation / termination / recycling / cryo-EM
Function / homology
Function and homology information


Eukaryotic Translation Termination / sno(s)RNA transcription / translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding / ribosome disassembly / peptidyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) ...Eukaryotic Translation Termination / sno(s)RNA transcription / translation release factor complex / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding / ribosome disassembly / peptidyl-tRNA hydrolase activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit binding / translational termination / ribosomal subunit export from nucleus / translation initiation factor activity / positive regulation of translation / ribosomal large subunit biogenesis / translational initiation / DNA-templated transcription termination / cytoplasmic stress granule / rRNA processing / iron ion binding / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...RLI, domain 1 / RLI1 / RNase L inhibitor RLI-like, possible metal-binding domain / Possible Fer4-like domain in RNase L inhibitor, RLI / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / 4Fe-4S binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / ABC transporter-like, conserved site / ABC transporters family signature. / 50S ribosomal protein L30e-like / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic peptide chain release factor subunit 1 / Translation initiation factor RLI1
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.75 Å
AuthorsPreis A / Heuer A / Barrio-Garcia C / Hauser A / Eyler D / Berninghausen O / Green R / Becker T / Beckmann R
CitationJournal: Cell Rep / Year: 2014
Title: Cryoelectron microscopic structures of eukaryotic translation termination complexes containing eRF1-eRF3 or eRF1-ABCE1.
Authors: Anne Preis / Andre Heuer / Clara Barrio-Garcia / Andreas Hauser / Daniel E Eyler / Otto Berninghausen / Rachel Green / Thomas Becker / Roland Beckmann /
Abstract: Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and ...Termination and ribosome recycling are essential processes in translation. In eukaryotes, a stop codon in the ribosomal A site is decoded by a ternary complex consisting of release factors eRF1 and guanosine triphosphate (GTP)-bound eRF3. After GTP hydrolysis, eRF3 dissociates, and ABCE1 can bind to eRF1-loaded ribosomes to stimulate peptide release and ribosomal subunit dissociation. Here, we present cryoelectron microscopic (cryo-EM) structures of a pretermination complex containing eRF1-eRF3 and a termination/prerecycling complex containing eRF1-ABCE1. eRF1 undergoes drastic conformational changes: its central domain harboring the catalytically important GGQ loop is either packed against eRF3 or swung toward the peptidyl transferase center when bound to ABCE1. Additionally, in complex with eRF3, the N-terminal domain of eRF1 positions the conserved NIKS motif proximal to the stop codon, supporting its suggested role in decoding, yet it appears to be delocalized in the presence of ABCE1. These results suggest that stop codon decoding and peptide release can be uncoupled during termination.
History
DepositionFeb 27, 2014-
Header (metadata) releaseMar 26, 2014-
Map releaseJul 16, 2014-
UpdateJul 23, 2014-
Current statusJul 23, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.232
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.232
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4crm
  • Surface level: 0.232
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4crm
  • Surface level: 0.232
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4crm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2598-Rli...

Downloads & links

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Map

FileDownload / File: emd_2598.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation"CMV-stalled" wheat germ 80S-RNC bound to eRF1 and ABCE1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å		1.24 Å/pix.
x 368 pix.
= 455.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.232 / Movie #1: 0.232
Minimum - Maximum-0.63350767 - 1.32882106
Average (Standard dev.)0.00894418 (±0.0960145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 455.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z455.400455.400455.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.6341.3290.009

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Supplemental data

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Sample components

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Entire : "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP

EntireName: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
Components
  • Sample: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
  • Complex: 80S ribosome
  • Protein or peptide: Sup45
  • Protein or peptide: Rli1

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Supramolecule #1000: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP

SupramoleculeName: "CMV"-stalled wheat germ 80S-RNC bound to eRF1 and ABCE1-ADPNP
type: sample / ID: 1000
Oligomeric state: One ribosome binds to one eRF1 and one ABCE1
Number unique components: 3

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Supramolecule #1: 80S ribosome

SupramoleculeName: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum aestivum (bread wheat) / synonym: Bread wheat / Tissue: seed

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Macromolecule #1: Sup45

MacromoleculeName: Sup45 / type: protein_or_peptide / ID: 1 / Name.synonym: eRF1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Location in cell: cytoplasm
Molecular weightTheoretical: 49 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pTYB2

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Macromolecule #2: Rli1

MacromoleculeName: Rli1 / type: protein_or_peptide / ID: 2 / Name.synonym: ABCE1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: cytoplasm
Molecular weightTheoretical: 68 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pYES2

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 200 mM KCl, 1.5 MgCl2, 2 mM DTT, 0.01 mg/ml cycloheximide, 0.05 % Nikkol, 0.03 % DBC, 0.5 mM ADPNP).
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Sec61 was added at a five-fold molar excess to saturate the hydrophobic signal-anchor sequence and avoid orientational bias on the cryo-grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateFeb 20, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 147136 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were picked with starfish_boxing version 0.2.0, which is part of the new StarFish single particle analysis program suite.
CTF correctionDetails: on volumes (SPIDER)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.75 Å / Resolution method: OTHER / Software - Name: StarFish, SPIDER / Details: Data-subset resulted from computational sorting / Number images used: 39309

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Atomic model buiding 1

Initial modelPDB ID:

1dt9

SoftwareName: Chimera, Coot, MDFF
DetailsA homology model of eRF1 was created using HHPred. The domains were separately fitted by manual docking using program Coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4crm:
Cryo-EM of a pre-recycling complex with eRF1 and ABCE1

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Atomic model buiding 2

Initial modelPDB ID:

3j16


Chain - Chain ID: B
SoftwareName: Chimera, Coot, MDFF
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4crm:
Cryo-EM of a pre-recycling complex with eRF1 and ABCE1

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