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- EMDB-2528: Arx1 pre-60S particle -

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Basic information

Entry
Database: EMDB / ID: EMD-2528
TitleArx1 pre-60S particle
Map dataCryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP.
Sample
  • Sample: TAP purification of Alb1-TAP from yeast.
  • Complex: Arx1 pre-60S particle
Keywordsribosome biogenesis / ribosome assembly / pre-60S / 5S RNP / assembly intermediate
Function / homology
Function and homology information


protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases / Antigen processing: Ubiquitination & Proteasome degradation / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...protein-RNA complex remodeling / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Hydrolases / Antigen processing: Ubiquitination & Proteasome degradation / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / maturation of SSU-rRNA / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Neutrophil degranulation / translation initiation factor activity / small-subunit processome / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / rRNA processing / ribosomal large subunit assembly / metallopeptidase activity / large ribosomal subunit rRNA binding / ribosome biogenesis / 5S rRNA binding / cytoplasmic translation / ATPase binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / proteolysis / RNA binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / NLE / NLE (NUC135) domain / Ribosome assembly factor Mrt4 / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) ...: / NLE / NLE (NUC135) domain / Ribosome assembly factor Mrt4 / NOG, C-terminal / Nucleolar GTP-binding protein 1 / NOGCT (NUC087) domain / Nucleolar GTP-binding protein 1, Rossman-fold domain / NOG1, N-terminal helical domain / Nucleolar GTP-binding protein 1 (NOG1) / NOG1 N-terminal helical domain / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Translation initiation factor IF6 / eIF-6 family / translation initiation factor 6 / Creatinase/aminopeptidase-like / GTP binding domain / : / 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 L27e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L38e protein family / Ribosomal protein L23/L25, N-terminal / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein L35Ae, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L34Ae / Ribosomal protein L23, N-terminal domain / Ribosomal protein L13e, conserved site / Ribosomal protein L13e signature. / Ribosomal L27e protein family / Ribosomal Protein L6, KOW domain / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L30/YlxQ / Ribosomal protein L34e / Ribosomal protein L31e, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L37ae / 60S ribosomal protein L6E / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein L7A/L8 / Ribosomal protein L27e signature. / Ribosomal protein L13e / Ribosomal protein L13e / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L6e / Ribosomal protein L19/L19e conserved site / Ribosomal L37ae protein family / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L35Ae / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L39e, conserved site / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L19e signature. / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L6e signature. / Ribosomal_L31e / Ribosomal protein L15e, conserved site / Ribosomal protein L30e signature 1. / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein 60S L18 and 50S L18e / Ribosomal protein L30e signature 2. / 60S ribosomal protein L19 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L3, domain 3, archaeal type superfamily / Ribosomal protein L3, archaeal/eukaryotic type / Ribosomal protein L36e signature. / Ribosomal protein L37e / Ribosomal protein L39e signature. / Ribosomal protein L21e / Ribosomal_L15e
Similarity search - Domain/homology
Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A ...Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL30A / Large ribosomal subunit protein uL6A / Large ribosomal subunit protein uL22A / Large ribosomal subunit protein uL24A / Large ribosomal subunit protein eL33A / Large ribosomal subunit protein eL36A / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Large ribosomal subunit protein eL20A / Large ribosomal subunit protein eL43A / Large ribosomal subunit protein uL14A / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2A / Large ribosomal subunit protein eL18A / Large ribosomal subunit protein uL11A / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein uL29A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / Ribosome assembly protein 4 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL13A / Ribosome assembly factor MRT4 / Large ribosomal subunit protein eL14A / Large ribosomal subunit protein eL32 / Ribosome biogenesis protein RLP7 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein eL34A / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / Nucleolar GTP-binding protein 1 / Probable metalloprotease ARX1 / Ribosome biogenesis protein RLP24 / Eukaryotic translation initiation factor 6 / Large ribosomal subunit protein eL13A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsLeidig C / Thoms M / Holdermann I / Bradatsch B / Berninghausen O / Bange G / Sinning I / Hurt E / Beckmann R
CitationJournal: Nat Commun / Year: 2014
Title: 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle.
Authors: Christoph Leidig / Matthias Thoms / Iris Holdermann / Bettina Bradatsch / Otto Berninghausen / Gert Bange / Irmgard Sinning / Ed Hurt / Roland Beckmann /
Abstract: During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed ...During eukaryotic ribosome biogenesis, nascent ribosomal RNA (rRNA) forms pre-ribosomal particles containing ribosomal proteins and assembly factors. Subsequently, these immature rRNAs are processed and remodelled. Little is known about the premature assembly states of rRNAs and their structural rearrangement during ribosome biogenesis. Using cryo-EM we characterize a pre-60S particle, where the 5S rRNA and its associated ribosomal proteins L18 and L5 (5S ribonucleoprotein (RNP)) are rotated by almost 180° when compared with the mature subunit. Consequently, neighbouring 25S rRNA helices that protrude from the base of the central protuberance are deformed. This altered topology is stabilized by nearby assembly factors (Rsa4 and Nog1), which were identified by fitting their three-dimensional structures into the cryo-EM density. We suggest that the 5S RNP performs a semicircular movement during 60S biogenesis to adopt its final position, fulfilling a chaperone-like function in guiding the flanking 25S rRNA helices of the central protuberance to their final topology.
History
DepositionDec 5, 2013-
Header (metadata) releaseDec 18, 2013-
Map releaseMar 26, 2014-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v7f
  • Surface level: 0.45
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2528.png

Downloads & links

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Map

FileDownload / File: emd_2528.map.gz / Format: CCP4 / Size: 264.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of an early yeast Arx1 pre-60S particle purified via Alb1-TAP.
Voxel sizeX=Y=Z: 1.0605 Å
Density
Contour LevelBy AUTHOR: 0.45 / Movie #1: 0.45
Minimum - Maximum-0.82164174 - 2.00969124
Average (Standard dev.)0.00647931 (±0.15501215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-207-207-206
Dimensions414414414
Spacing414414414
CellA=B=C: 439.047 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06051.06051.0605
M x/y/z414414414
origin x/y/z0.0000.0000.000
length x/y/z439.047439.047439.047
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S213
start NC/NR/NS-207-207-206
NC/NR/NS414414414
D min/max/mean-0.8222.0100.006

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Supplemental data

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Sample components

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Entire : TAP purification of Alb1-TAP from yeast.

EntireName: TAP purification of Alb1-TAP from yeast.
Components
  • Sample: TAP purification of Alb1-TAP from yeast.
  • Complex: Arx1 pre-60S particle

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Supramolecule #1000: TAP purification of Alb1-TAP from yeast.

SupramoleculeName: TAP purification of Alb1-TAP from yeast. / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Arx1 pre-60S particle

SupramoleculeName: Arx1 pre-60S particle / type: complex / ID: 1 / Recombinant expression: No
Ribosome-details: ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast

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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

VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateNov 12, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 5686 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: OTHER / Number images used: 75887

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Atomic model buiding 1

Initial modelPDB ID:

3u5d
PDB Unreleased entry


Chain - #0 - Chain ID: 1 / Chain - #1 - Chain ID: 3 / Chain - #2 - Chain ID: 4
DetailsThe coordinates were initially fitted by rigid body fitting before the structure was manually adjusted to the density and refined using molecular dynamics simulations.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v7f:
Arx1 pre-60S particle.

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Atomic model buiding 2

Initial modelPDB ID:

3u5e
PDB Unreleased entry


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: J / Chain - #9 - Chain ID: L / Chain - #10 - Chain ID: M / Chain - #11 - Chain ID: N / Chain - #12 - Chain ID: O / Chain - #13 - Chain ID: P / Chain - #14 - Chain ID: Q / Chain - #15 - Chain ID: R / Chain - #16 - Chain ID: S / Chain - #17 - Chain ID: T / Chain - #18 - Chain ID: U / Chain - #19 - Chain ID: V / Chain - #20 - Chain ID: X / Chain - #21 - Chain ID: Y / Chain - #22 - Chain ID: Z / Chain - #23 - Chain ID: a / Chain - #24 - Chain ID: c / Chain - #25 - Chain ID: d / Chain - #26 - Chain ID: e / Chain - #27 - Chain ID: f / Chain - #28 - Chain ID: g / Chain - #29 - Chain ID: h / Chain - #30 - Chain ID: i / Chain - #31 - Chain ID: j / Chain - #32 - Chain ID: k / Chain - #33 - Chain ID: l / Chain - #34 - Chain ID: p
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v7f:
Arx1 pre-60S particle.

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Atomic model buiding 3

Initial modelPDB ID:

3izs
PDB Unreleased entry


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: J
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v7f:
Arx1 pre-60S particle.

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Atomic model buiding 4

Initial modelPDB ID:

4b6a
PDB Unreleased entry


Chain - Chain ID: t
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v7f:
Arx1 pre-60S particle.

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Atomic model buiding 5

Initial modelPDB ID:

1g62


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v7f:
Arx1 pre-60S particle.

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