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- EMDB-2009: 3D reconstruction of an archaeal 70S ribosome in complex with aPe... -

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Entry
Database: EMDB / ID: EMD-2009
Title3D reconstruction of an archaeal 70S ribosome in complex with aPelota and aABCE1
Map dataThis is a 3D cryo-EM reconstruction of a Pyrococcus furiosus 70S ribosome in complex with aABCE1 and aPelota
Sample
  • Sample: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
  • Complex: Pyrococcus furiosus 70S ribosome
  • Protein or peptide: aABCE1
  • Protein or peptide: aPelota
Keywordstranslation / ribosome recycling / no-go mRNA decay
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / rRNA processing / large ribosomal subunit rRNA binding ...RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / ribosome disassembly / ribonuclease P activity / tRNA 5'-leader removal / cytosolic ribosome / rRNA processing / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / endonuclease activity / tRNA binding / Hydrolases; Acting on ester bonds / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
: / Translation release factor pelota, archaea / : / : / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Ribosomal protein L14e / Ribosomal protein L1, archaea / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal ...: / Translation release factor pelota, archaea / : / : / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Ribosomal protein L14e / Ribosomal protein L1, archaea / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / 50S ribosomal protein L10, archaea / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Ribosomal protein L23 / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / metallochaperone-like domain / TRASH domain / Ribosomal protein S19e, conserved site / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S4e, N-terminal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein S8e
Similarity search - Domain/homology
Small ribosomal subunit protein uS10 / 30S ribosomal protein S4 / 30S ribosomal protein S12 / Protein pelota homolog / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / 50S ribosomal protein L37Ae / 50S ribosomal protein L10 / 50S ribosomal protein L1 / 50S ribosomal protein L11 ...Small ribosomal subunit protein uS10 / 30S ribosomal protein S4 / 30S ribosomal protein S12 / Protein pelota homolog / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein eS1 / 50S ribosomal protein L37Ae / 50S ribosomal protein L10 / 50S ribosomal protein L1 / 50S ribosomal protein L11 / Large ribosomal subunit protein eL33 / 50S ribosomal protein L3 / 50S ribosomal protein L4 / 50S ribosomal protein L23 / 50S ribosomal protein L2 / Small ribosomal subunit protein uS19 / 50S ribosomal protein L22 / Small ribosomal subunit protein uS3 / 50S ribosomal protein L29 / Small ribosomal subunit protein uS17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / Small ribosomal subunit protein eS4 / 50S ribosomal protein L5 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / 50S ribosomal protein L6 / 50S ribosomal protein L19e / Small ribosomal subunit protein uS5 / 50S ribosomal protein L15 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS11 / 50S ribosomal protein L18e / 50S ribosomal protein L13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2 / 50S ribosomal protein L30e / Small ribosomal subunit protein uS7 / 50S ribosomal protein L37e / 30S ribosomal protein S19e / Small ribosomal subunit protein eS17 / 50S ribosomal protein L40e / 50S ribosomal protein L24e / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS8 / 50S ribosomal protein L21e / Small ribosomal subunit protein eS32 / 50S ribosomal protein L15e / 50S ribosomal protein L34e / 50S ribosomal protein L14e / Small ribosomal subunit protein eS6 / 50S ribosomal protein L39e / 50S ribosomal protein L31e / 50S ribosomal protein L18Ae / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS27 / 50S ribosomal protein L44e / 50S ribosomal protein L30 / 50S ribosomal protein L18 / 50S ribosomal protein L32e / 50S ribosomal protein L10e
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea) / Thermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.6 Å
AuthorsBecker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I ...Becker T / Franckenberg S / Wickles S / Shoemaker CJ / Anger AM / Armache J-P / Sieber H / Ungewickell C / Berninghausen O / Daberkow I / Karcher A / Thomm M / Hopfner K-P / Green R / Beckmann R
CitationJournal: Nature / Year: 2012
Title: Structural basis of highly conserved ribosome recycling in eukaryotes and archaea.
Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo ...Authors: Thomas Becker / Sibylle Franckenberg / Stephan Wickles / Christopher J Shoemaker / Andreas M Anger / Jean-Paul Armache / Heidemarie Sieber / Charlotte Ungewickell / Otto Berninghausen / Ingo Daberkow / Annette Karcher / Michael Thomm / Karl-Peter Hopfner / Rachel Green / Roland Beckmann /
Abstract: Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation ...Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron-sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.
History
DepositionDec 10, 2011-
Header (metadata) releaseFeb 15, 2012-
Map releaseFeb 17, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j15
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j15
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j15, PDB-4v6u
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j15
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v6u
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMBD_2009.gif

Downloads & links

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Map

FileDownload / File: emd_2009.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3D cryo-EM reconstruction of a Pyrococcus furiosus 70S ribosome in complex with aABCE1 and aPelota
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.49689907 - 0.74534863
Average (Standard dev.)0.00440064 (±0.04026932)
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-0.4970.7450.004

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Supplemental data

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Sample components

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Entire : Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1

EntireName: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
Components
  • Sample: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
  • Complex: Pyrococcus furiosus 70S ribosome
  • Protein or peptide: aABCE1
  • Protein or peptide: aPelota

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Supramolecule #1000: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1

SupramoleculeName: Pyrococcus furiosus 70S ribosome in complex with aPelota and aABCE1
type: sample / ID: 1000
Oligomeric state: One 70S ribosome binds one aPelota and one aABCE1
Number unique components: 3

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Supramolecule #1: Pyrococcus furiosus 70S ribosome

SupramoleculeName: Pyrococcus furiosus 70S ribosome / type: complex / ID: 1 / Name.synonym: Pyrococcus furiosus 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Pyrococcus furiosus (archaea)

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Macromolecule #1: aABCE1

MacromoleculeName: aABCE1 / type: protein_or_peptide / ID: 1 / Name.synonym: ABCE1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Pyrococcus furiosus (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: aPelota

MacromoleculeName: aPelota / type: protein_or_peptide / ID: 2 / Name.synonym: Pelota / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Thermococcus kodakarensis (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28

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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: 8.2
Details: 56 mM Tris pH 8.2, 250 mM KOAc, 80 mM NH4OAc, 50 mM MgCl2, 1 mM DTT, 2 mM ADPNP
StainingType: NEGATIVE / Details: cryo-EM
GridDetails: Quantifoil grids (3/3) with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blot for 10 seconds before plunging, use 2 layer of filter paper

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder: autoloader / Specimen holder model: OTHER
DetailsFinal magnification of the object on the CCD image is 148721
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 10000 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Wiener Filter
Final angle assignmentDetails: SPIDER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: sorting for ribosome conformation and ligand presence was performed
Number images used: 51000

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Atomic model buiding 1

Initial modelPDB ID:

3bk7


Chain - Chain ID: A
SoftwareName: MDFF
DetailsPDBEntryID_givenInChain. Protocol: rigid body followed by molecular dynamics flexible fitting. rigid body fitting of individual domains followed by molecular dynamics flexible fitting
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j15:
Model of ribosome-bound archaeal Pelota and ABCE1

PDB-4v6u:
Promiscuous behavior of proteins in archaeal ribosomes revealed by cryo-EM: implications for evolution of eukaryotic ribosomes

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