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- EMDB-1669: Cryo-EM structures of the idle yeast Ssh1 complex bound to the ye... -

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Entry
Database: EMDB / ID: EMD-1669
TitleCryo-EM structures of the idle yeast Ssh1 complex bound to the yeast 80S ribosome
Map dataThis map represents a yeast 80S ribosome bound to the idle yeast Ssh1 complex
Sample
  • Sample: An idle yeast Ssh1 complex bound to a yeast 80S ribosome
  • Complex: Yeast 80S ribosome bound to the yeast Ssh1 complex
  • Ligand: Ssh1 complex
KeywordsRibosome / protein exit tunnel / cotranslational protein translocation / protein conducting channel / signal sequence
Function / homology
Function and homology information


translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / SRP-dependent cotranslational protein targeting to membrane, translocation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / signal sequence binding / Protein methylation ...translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / SRP-dependent cotranslational protein targeting to membrane, translocation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / signal sequence binding / Protein methylation / SRP-dependent cotranslational protein targeting to membrane / RMTs methylate histone arginines / positive regulation of translational fidelity / post-translational protein targeting to membrane, translocation / GDP-dissociation inhibitor activity / ribosome-associated ubiquitin-dependent protein catabolic process / Protein hydroxylation / : / nuclear inner membrane / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / translational elongation / response to cycloheximide / protein kinase activator activity / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translation regulator activity / protein transmembrane transporter activity / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / 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) / regulation of translational fidelity / ribonucleoprotein complex binding / rescue of stalled ribosome / translational termination / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / guanyl-nucleotide exchange factor activity / protein kinase C binding / maintenance of translational fidelity / macroautophagy / modification-dependent protein catabolic process / ribosomal small subunit biogenesis / protein tag activity / small ribosomal subunit rRNA binding / rRNA processing / ribosomal small subunit assembly / cytoplasmic stress granule / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / negative regulation of translation / protein ubiquitination / rRNA binding / ribosome / structural constituent of ribosome / positive regulation of protein phosphorylation / translation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / mitochondrion / RNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. ...Ribosomal protein L12/P1/P2 family / Ribosomal protein P1/P2, N-terminal domain / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / 60s Acidic ribosomal protein / 60S acidic ribosomal protein P0 / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Small (40S) ribosomal subunit Asc1/RACK1 / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S17e, conserved site / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / S25 ribosomal protein / Ribosomal protein L10e, conserved site / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein L10e / Ribosomal protein L27e, conserved site / Ribosomal protein S19A/S15e / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / 40S ribosomal protein S11, N-terminal / Ribosomal protein L1, conserved site / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein S19e, conserved site / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein L44e / Ribosomal protein L38e / Ribosomal protein S2, eukaryotic / Ribosomal protein L38e superfamily / Ribosomal protein L27e / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein S21e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal L38e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / 60S ribosomal protein L35 / Ribosomal protein L1 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S27 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S28e conserved site / Ribosomal protein S28e / Ribosomal protein L35Ae, conserved site / Ribosomal_S17 N-terminal / Ribosomal protein L44 / Ribosomal L27e protein family / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein L31e, conserved site / Ribosomal protein L1 signature. / Ribosomal protein L37ae / Ribosomal protein S27 / Ribosomal protein L19, eukaryotic / Ribosomal protein L35A / Ribosomal protein S17e signature. / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal L40e family / Ribosomal protein L36e / Ribosomal protein L35A superfamily / Ribosomal protein S28e / Ribosomal protein L44e signature. / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L27e signature.
Similarity search - Domain/homology
60S ribosomal protein L14-A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 ...60S ribosomal protein L14-A / Small ribosomal subunit protein uS4A / 60S ribosomal protein L42-A / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein eS17A / Large ribosomal subunit protein eL24A / 60S ribosomal protein L23-B / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein P1A / 60S acidic ribosomal protein P2-alpha / 60S ribosomal protein L19-A / 60S ribosomal protein L2-A / 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 / 60S ribosomal protein L41-B / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein eL15A / Large ribosomal subunit protein eL22A / Small ribosomal subunit protein uS3 / 40S ribosomal protein S4-B / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS11A / 60S ribosomal protein L18-A / Small ribosomal subunit protein eS19A / Small ribosomal subunit protein eS21A / Small ribosomal subunit protein uS8A / Large ribosomal subunit protein uL5A / Large ribosomal subunit protein eL27A / Large ribosomal subunit protein eL31A / Ubiquitin-ribosomal protein eL40A fusion protein / Large ribosomal subunit protein eL43B / Large ribosomal subunit protein eL42B / Small ribosomal subunit protein uS12B / 40S ribosomal protein S24-B / Small ribosomal subunit protein eS30A / Small ribosomal subunit protein eS4A / Large ribosomal subunit protein uL14B / Large ribosomal subunit protein uL1A / Large ribosomal subunit protein uL2B / Small ribosomal subunit protein uS17B / Large ribosomal subunit protein eL18B / Small ribosomal subunit protein uS9B / Large ribosomal subunit protein uL11A / Small ribosomal subunit protein uS13B / Large ribosomal subunit protein eL19A / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL29A / Small ribosomal subunit protein eS32A / Large ribosomal subunit protein uL4A / Large ribosomal subunit protein eL30 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL8A / 60S ribosomal protein L12-A / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / 40S ribosomal protein S11-B / 40S ribosomal protein S24-B / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL13A / 40S ribosomal protein S23-A / Small ribosomal subunit protein uS2A / Protein transport protein SSS1 / 40S ribosomal protein S18-A / Small ribosomal subunit protein eS27A / Large ribosomal subunit protein eL14A / Small ribosomal subunit protein RACK1 / Large ribosomal subunit protein eL32 / Sec sixty-one protein homolog / Small ribosomal subunit protein uS10 / 60S ribosomal protein L35-A / 40S ribosomal protein S16-B / Small ribosomal subunit protein uS14A / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein eL37A / Large ribosomal subunit protein eL38 / Large ribosomal subunit protein uL4B / 60S ribosomal protein L43-A / Protein transport protein SBH2 / 60S ribosomal protein L1-B / Large ribosomal subunit protein eL34A / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein eL6A / Large ribosomal subunit protein eL21A / 60S ribosomal protein L18a / 40S ribosomal protein S30-A / Small ribosomal subunit protein eS25A / Small ribosomal subunit protein eS28A / 60S ribosomal protein L18a
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.8 Å
AuthorsBecker T / Mandon E / Bhushan S / Jarasch A / Armache JP / Funes S / Jossinet F / Gumbart J / Mielke T / Berninghausen O ...Becker T / Mandon E / Bhushan S / Jarasch A / Armache JP / Funes S / Jossinet F / Gumbart J / Mielke T / Berninghausen O / Schulten K / Westhof E / Gilmore R / Beckmann R
CitationJournal: Science / Year: 2009
Title: Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
Authors: Thomas Becker / Shashi Bhushan / Alexander Jarasch / Jean-Paul Armache / Soledad Funes / Fabrice Jossinet / James Gumbart / Thorsten Mielke / Otto Berninghausen / Klaus Schulten / Eric ...Authors: Thomas Becker / Shashi Bhushan / Alexander Jarasch / Jean-Paul Armache / Soledad Funes / Fabrice Jossinet / James Gumbart / Thorsten Mielke / Otto Berninghausen / Klaus Schulten / Eric Westhof / Reid Gilmore / Elisabet C Mandon / Roland Beckmann /
Abstract: The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may ...The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. Although Sec complexes can form oligomers, it has been suggested that a single copy may serve as an active PCC. We determined subnanometer-resolution cryo-electron microscopy structures of eukaryotic ribosome-Sec61 complexes. In combination with biochemical data, we found that in both idle and active states, the Sec complex is not oligomeric and interacts mainly via two cytoplasmic loops with the universal ribosomal adaptor site. In the active state, the ribosomal tunnel and a central pore of the monomeric PCC were occupied by the nascent chain, contacting loop 6 of the Sec complex. This provides a structural basis for the activity of a solitary Sec complex in cotranslational protein translocation.
History
DepositionDec 3, 2009-
Header (metadata) releaseDec 16, 2009-
Map releaseDec 22, 2010-
UpdateMay 24, 2012-
Current statusMay 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.75
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  • Surface view colored by height
  • Surface level: 1.75
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  • Surface view with fitted model
  • Atomic models: PDB-2wwa
  • Surface level: 1.75
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  • Surface view with fitted model
  • Atomic models: PDB-4v6i
  • Surface level: 1.75
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2wwa
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izd
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v6i
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Movie viewer
Structure viewerEM map:
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Supplemental images

1669.gif

1669_EMD_166...

Downloads & links

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Map

FileDownload / File: emd_1669.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis map represents a yeast 80S ribosome bound to the idle yeast Ssh1 complex
Voxel sizeX=Y=Z: 1.2375 Å
Density
Contour LevelBy AUTHOR: 1.75 / Movie #1: 1.75
Minimum - Maximum-3.67190695 - 7.74682808
Average (Standard dev.)0.04872083 (±0.60868454)
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-3.6727.7470.049

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Supplemental data

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Sample components

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Entire : An idle yeast Ssh1 complex bound to a yeast 80S ribosome

EntireName: An idle yeast Ssh1 complex bound to a yeast 80S ribosome
Components
  • Sample: An idle yeast Ssh1 complex bound to a yeast 80S ribosome
  • Complex: Yeast 80S ribosome bound to the yeast Ssh1 complex
  • Ligand: Ssh1 complex

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Supramolecule #1000: An idle yeast Ssh1 complex bound to a yeast 80S ribosome

SupramoleculeName: An idle yeast Ssh1 complex bound to a yeast 80S ribosome
type: sample / ID: 1000
Details: 80S ribosomes and the detergent solubilized Ssh1 complex were reconstituted in vitro by adding 1 pmol of ribosome and Ssh1 complex in 5 fold molar excess
Oligomeric state: 80S Ribosome bound to one copy of the heterotrimeric Ssh1 complex
Number unique components: 2
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa / Method: Known for 80S ribosomes

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Supramolecule #1: Yeast 80S ribosome bound to the yeast Ssh1 complex

SupramoleculeName: Yeast 80S ribosome bound to the yeast Ssh1 complex / type: complex / ID: 1
Name.synonym: Yeast 80S ribosome bound to the yeast Ssh1 complex
Ribosome-details: ribosome-eukaryote: ALL
Molecular weightExperimental: 4.2 MDa / Theoretical: 4.2 MDa

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Macromolecule #1: Ssh1 complex

MacromoleculeName: Ssh1 complex / type: ligand / ID: 1 / Name.synonym: Ssh1 complex / Details: His FLAG-tagged / Number of copies: 1 / Oligomeric state: Heterotrimer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: RGY1592 / synonym: Baker's yeast / Cell: Rough microsomes / Organelle: Endoplasmic reticulum membrane / Location in cell: Endoplasmic reticulum
Molecular weightTheoretical: 71.5 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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/KOH, pH 7.5 100 mM KOAc, 10 mM Mg(OAc)2, 1.5 mM DTT, 0.1 % (w/v) digitonin
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 POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara cartridge system / Specimen holder model: OTHER
TemperatureAverage: 84 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.76 µm / Number real images: 185 / Average electron dose: 25 e/Å2 / Details: Scanned at 5334 dpi / Od range: 1.2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus group volumes
Final angle assignmentDetails: SPIDER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER
Details: Map was filtered between 8.3 and 10.3 Angstrom to better visualize the Ssh1 complex
Number images used: 20400
DetailsParticles were selected using the program SIGNATURE and visually inspected. This map resulted from sorting against the ES27 exit position and subsequent sorting for tRNA and the Ssh1 complex and represents the datasubset with the Ssh1 complex present without tRNA.

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