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- EMDB-2012: The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Co... -

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Basic information

Entry
Database: EMDB / ID: EMD-2012
TitleThe Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6
Map dataStructure of the M. thermautotrophicus 50S-aIF6 complex
Sample
  • Sample: 50S ribosomal subunit in complex with archaeal initiation factor 6
  • Complex: Methanothermobacter thermautotrophicus 50S ribosomal subunit
  • Protein or peptide: aIF6
Keywords50S ribosomal subunit / protein synthesis / initiation factor 6
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / cytosolic ribosome / cytosolic ribosome assembly / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleotide binding / DNA repair / DNA binding / RNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal protein L19e, domain 2 / Ribosomal protein L19e, domain 3 / 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 L19e, domain 2 / Ribosomal protein L19e, domain 3 / 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 / Translation initiation factor IF6 / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / DNA repair Rad51/transcription factor NusA, alpha-helical / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Helix-hairpin-helix domain / Ribosomal protein L23 / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / metallochaperone-like domain / TRASH domain / Ribosomal protein L44e / Ribosomal protein L44 / Ribosomal protein L31e, conserved site / Ribosomal protein L37ae / Ribosomal L40e family / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal protein L10e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L19e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L24e, conserved site / Ribosomal protein L24e signature. / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L34Ae / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L34e / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / 60S ribosomal protein L19 / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal protein L31e / Ribosomal protein L37ae/L37e / Ribosomal protein L6, conserved site-2 / Ribosomal protein L30/YlxQ / Ribosomal protein L18/L18-A/B/e, conserved site / Ribosomal protein L18e signature. / Ribosomal protein L39e / Ribosomal protein L26/L24, eukaryotic/archaeal / Ribosomal protein L39e domain superfamily / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e / Ribosomal protein L18e / Ribosomal L39 protein / Ribosomal protein L37e / Ribosomal L15 / Ribosomal protein L31e signature. / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14
Similarity search - Domain/homology
Large ribosomal subunit protein eL20 / Translation initiation factor 6 / Large ribosomal subunit protein eL34 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 ...Large ribosomal subunit protein eL20 / Translation initiation factor 6 / Large ribosomal subunit protein eL34 / Ubiquitin-ribosomal protein eL40 fusion protein / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL18 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein eL14
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus str. Delta H (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.6 Å
AuthorsGreber BJ / Boehringer D / Godinic-Mikulcic V / Crnkovic A / Ibba M / Weygand-Durasevic I / Ban N
CitationJournal: J Mol Biol / Year: 2012
Title: Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution.
Authors: Basil J Greber / Daniel Boehringer / Vlatka Godinic-Mikulcic / Ana Crnkovic / Michael Ibba / Ivana Weygand-Durasevic / Nenad Ban /
Abstract: Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains ...Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea.
History
DepositionDec 20, 2011-
Header (metadata) releaseJan 31, 2012-
Map releaseJan 31, 2012-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 30
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 30
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4adx
  • Surface level: 30
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD2012_imag...

Downloads & links

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Map

FileDownload / File: emd_2012.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the M. thermautotrophicus 50S-aIF6 complex
Voxel sizeX=Y=Z: 1.81 Å
Density
Contour LevelBy AUTHOR: 30.0 / Movie #1: 30
Minimum - Maximum-201.715789790000002 - 276.055297849999988
Average (Standard dev.)-10.795081140000001 (±22.579296110000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 325.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z325.800325.800325.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-201.716276.055-10.795

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Supplemental data

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Segmentation: NONE

AnnotationNONE
Fileemd_2012_msk_1.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 : 50S ribosomal subunit in complex with archaeal initiation factor 6

EntireName: 50S ribosomal subunit in complex with archaeal initiation factor 6
Components
  • Sample: 50S ribosomal subunit in complex with archaeal initiation factor 6
  • Complex: Methanothermobacter thermautotrophicus 50S ribosomal subunit
  • Protein or peptide: aIF6

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Supramolecule #1000: 50S ribosomal subunit in complex with archaeal initiation factor 6

SupramoleculeName: 50S ribosomal subunit in complex with archaeal initiation factor 6
type: sample / ID: 1000 / Details: none / Oligomeric state: Equimolar complex of 50S and aIF6 / Number unique components: 2
Molecular weightTheoretical: 1.6 MDa

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Supramolecule #1: Methanothermobacter thermautotrophicus 50S ribosomal subunit

SupramoleculeName: Methanothermobacter thermautotrophicus 50S ribosomal subunit
type: complex / ID: 1 / Name.synonym: Large ribosomal subunit / Recombinant expression: No
Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S
Source (natural)Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea)
Location in cell: Cytoplasm
Molecular weightTheoretical: 1.6 MDa

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Macromolecule #1: aIF6

MacromoleculeName: aIF6 / type: protein_or_peptide / ID: 1 / Name.synonym: archaeal initiation factor 6 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea)
Location in cell: Cytoplasm
Molecular weightTheoretical: 23 KDa
SequenceUniProtKB: Translation initiation factor 6 / InterPro: Translation initiation factor IF6

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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 / Details: 20 mM Tris-HCl pH 8, 20 mM MgCl2, 50 mM NH4Cl
StainingType: NEGATIVE / Details: cryo
GridDetails: Quantifoil holey carbon grid R2/1
VitrificationCryogen name: ETHANE / Chamber temperature: 80 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger / Method: manual blotting

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Electron microscopy

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 83000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 87 K
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: per frame
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: Imagic-5, SPIDER / Number images used: 70364

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Atomic model buiding 1

Initial modelPDB ID:

3cc2

SoftwareName: Chimera
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4adx:
The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

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Atomic model buiding 2

Initial modelPDB ID:

3o58
PDB Unreleased entry

SoftwareName: Chimera
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4adx:
The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

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Atomic model buiding 3

Initial modelPDB ID:

4a17
PDB Unreleased entry

SoftwareName: Chimera
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4adx:
The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

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Atomic model buiding 4

Initial modelPDB ID:

4a19
PDB Unreleased entry

SoftwareName: Chimera
DetailsProtocol: rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation
Output model

PDB-4adx:
The Cryo-EM Structure of the Archaeal 50S Ribosomal Subunit in Complex with Initiation Factor 6

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