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- EMDB-12867: Structure of a human mitochondrial ribosome large subunit assembl... -

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Basic information

Entry
Database: EMDB / ID: EMD-12867
TitleStructure of a human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.
Map dataGlobal refinement map.
Sample
  • Complex: Human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.
    • Protein or peptide: x 54 types
    • RNA: x 2 types
  • Ligand: x 3 types
Function / homology
Function and homology information


negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational termination / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial translational termination / iron-sulfur cluster assembly complex / mitochondrial large ribosomal subunit binding / protein lipoylation / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial translational elongation / mitochondrial fission / [2Fe-2S] cluster assembly / aminoacyl-tRNA hydrolase / Glyoxylate metabolism and glycine degradation / mitochondrial large ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial small ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / acyl binding / mitochondrial ribosome / acyl carrier activity / iron-sulfur cluster assembly / mitochondrial translation / ribosomal large subunit binding / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / anatomical structure morphogenesis / aerobic respiration / ribosomal large subunit biogenesis / fatty acid binding / cellular response to leukemia inhibitory factor / ribosome assembly / mitochondrial membrane / small ribosomal subunit rRNA binding / fibrillar center / fatty acid biosynthetic process / large ribosomal subunit rRNA binding / rRNA processing / double-stranded RNA binding / ribosome binding / ribosome biogenesis / large ribosomal subunit / cell junction / 5S rRNA binding / ribosomal large subunit assembly / cellular response to hypoxia / negative regulation of translation / endonuclease activity / mitochondrial inner membrane / ribosome / rRNA binding / nuclear body / mitochondrial matrix / structural constituent of ribosome / translation / cell cycle / ribonucleoprotein complex / nucleotide binding / protein domain specific binding / mRNA binding / synapse / apoptotic process / GTP binding / calcium ion binding / nucleolus / mitochondrion / RNA binding / extracellular space / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation ...GTPase HflX / GTPase HflX, N-terminal / HflX-type guanine nucleotide-binding (G) domain / GTP-binding protein, middle domain / GTPase HflX, N-terminal domain superfamily / GTP-binding GTPase N-terminal / GTP-binding GTPase Middle Region / HflX-type guanine nucleotide-binding (G) domain profile. / MIEF1-MP, LYR domain / Ribosomal silencing factor during starvation / Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 superfamily / Mitochondrial ribosomal protein L55 / Ribosomal protein L37, mitochondrial / Mitochondrial ribosomal protein L48 / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L37 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S30, mitochondrial / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L53/MRP-L53 / 39S ribosomal protein L42, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Ribosomal protein L28/L40, mitochondrial / Mitochondrial ribosomal protein L28 / Ribosomal protein L37/S30 / Ribosomal protein 63, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Mitochondrial ribosomal subunit / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / Tim44-like domain / Tim44-like domain / Tim44 / MRPL44, double-stranded RNA binding domain / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS domain profile. / TGS / TGS-like / Ribonuclease III / 50S ribosome-binding GTPase / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / GTP binding domain / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Complex 1 LYR protein domain / Complex 1 protein (LYR family) / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / Beta-grasp domain superfamily / NTF2-like domain superfamily / NUDIX hydrolase-like domain superfamily / Ribosomal protein L11, bacterial-type / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L10P / Nucleotidyltransferase superfamily / Phosphopantetheine attachment site / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Putative GTP-binding protein 6 / 39S ribosomal protein L33, mitochondrial / 39S ribosomal protein L3, mitochondrial / 39S ribosomal protein L19, mitochondrial / 39S ribosomal protein L28, mitochondrial / 39S ribosomal protein L49, mitochondrial / Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L23, mitochondrial ...Mitochondrial ribosome and complex I assembly factor AltMIEF1 / Acyl carrier protein, mitochondrial / Putative GTP-binding protein 6 / 39S ribosomal protein L33, mitochondrial / 39S ribosomal protein L3, mitochondrial / 39S ribosomal protein L19, mitochondrial / 39S ribosomal protein L28, mitochondrial / 39S ribosomal protein L49, mitochondrial / Peptidyl-tRNA hydrolase ICT1, mitochondrial / 39S ribosomal protein L23, mitochondrial / 39S ribosomal protein L51, mitochondrial / 39S ribosomal protein L2, mitochondrial / 39S ribosomal protein L54, mitochondrial / 39S ribosomal protein L14, mitochondrial / 39S ribosomal protein L21, mitochondrial / 39S ribosomal protein L55, mitochondrial / 39S ribosomal protein L10, mitochondrial / 39S ribosomal protein L52, mitochondrial / 39S ribosomal protein L41, mitochondrial / 39S ribosomal protein L50, mitochondrial / 39S ribosomal protein L43, mitochondrial / Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L30, mitochondrial / 39S ribosomal protein L24, mitochondrial / 39S ribosomal protein L38, mitochondrial / Mitochondrial assembly of ribosomal large subunit protein 1 / 39S ribosomal protein L53, mitochondrial / 39S ribosomal protein L48, mitochondrial / 39S ribosomal protein L34, mitochondrial / Ribosomal protein 63, mitochondrial / 39S ribosomal protein L45, mitochondrial / 39S ribosomal protein L32, mitochondrial / 39S ribosomal protein L20, mitochondrial / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L9, mitochondrial / 39S ribosomal protein L4, mitochondrial / 39S ribosomal protein L37, mitochondrial / 39S ribosomal protein L18, mitochondrial / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein L44, mitochondrial / 39S ribosomal protein L47, mitochondrial / 39S ribosomal protein S30, mitochondrial / 39S ribosomal protein L40, mitochondrial / 39S ribosomal protein L17, mitochondrial / 39S ribosomal protein S18a, mitochondrial / 39S ribosomal protein L22, mitochondrial / 39S ribosomal protein L16, mitochondrial / 39S ribosomal protein L39, mitochondrial / 39S ribosomal protein L35, mitochondrial / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L36, mitochondrial / 39S ribosomal protein L27, mitochondrial / 39S ribosomal protein L11, mitochondrial / 39S ribosomal protein L42, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHillen HS / Lavdovskaia E / Nadler F / Hanitsch E / Linden A / Bohnsack KE / Urlaub H / Richter-Dennerlein R
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)RI 2715/1-1 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SFB1160 Germany
Citation
Journal: Nat Commun / Year: 2021
Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling.
Authors: Hauke S Hillen / Elena Lavdovskaia / Franziska Nadler / Elisa Hanitsch / Andreas Linden / Katherine E Bohnsack / Henning Urlaub / Ricarda Richter-Dennerlein /
Abstract: Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by ...Ribosome biogenesis requires auxiliary factors to promote folding and assembly of ribosomal proteins and RNA. Particularly, maturation of the peptidyl transferase center (PTC) is mediated by conserved GTPases, but the molecular basis is poorly understood. Here, we define the mechanism of GTPase-driven maturation of the human mitochondrial large ribosomal subunit (mtLSU) using endogenous complex purification, in vitro reconstitution and cryo-EM. Structures of transient native mtLSU assembly intermediates that accumulate in GTPBP6-deficient cells reveal how the biogenesis factors GTPBP5, MTERF4 and NSUN4 facilitate PTC folding. Addition of recombinant GTPBP6 reconstitutes late mtLSU biogenesis in vitro and shows that GTPBP6 triggers a molecular switch and progression to a near-mature PTC state. Additionally, cryo-EM analysis of GTPBP6-treated mature mitochondrial ribosomes reveals the structural basis for the dual-role of GTPBP6 in ribosome biogenesis and recycling. Together, these results provide a framework for understanding step-wise PTC folding as a critical conserved quality control checkpoint.
#1: Journal: Biorxiv / Year: 2021
Title: Structural basis of GTPase-mediated mitochondrial ribosome biogenesis and recycling
Authors: Hillen HS / Lavdovskaia E / Nadler F / Hanitsch E / Linden A / Bohnsack KE / Urlaub H / Richter-Dennerlein R
History
DepositionMay 4, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateJun 30, 2021-
Current statusJun 30, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0036
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7of2
  • Surface level: 0.0036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12867.png

Downloads & links

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Map

FileDownload / File: emd_12867.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal refinement map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 350 pix.
= 367.5 Å		1.05 Å/pix.
x 350 pix.
= 367.5 Å		1.05 Å/pix.
x 350 pix.
= 367.5 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0036 / Movie #1: 0.0036
Minimum - Maximum-0.016248722 - 0.0522895
Average (Standard dev.)-0.000103510465 (±0.0021008335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 367.49997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z367.500367.500367.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ560560560
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0160.052-0.000

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Supplemental data

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Mask #1

Fileemd_12867_msk_1.map
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Additional map: Post-processed map.

Fileemd_12867_additional_1.map
AnnotationPost-processed map.
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Half map: Refinement half-map 1.

Fileemd_12867_half_map_1.map
AnnotationRefinement half-map 1.
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AxesZYX

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Half map: Refinement half-map 2.

Fileemd_12867_half_map_2.map
AnnotationRefinement half-map 2.
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Sample components

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Entire : Human mitochondrial ribosome large subunit assembly intermediate ...

EntireName: Human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.
Components
  • Complex: Human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.
    • Protein or peptide: 39S ribosomal protein L32, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L33, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L34, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L35, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L36, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L37, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L38, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L39, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L40, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L41, mitochondrialRibosome
    • RNA: 16S ribosomal RNA
    • RNA: mitochondrial tRNAVal
    • Protein or peptide: Putative GTP-binding protein 6
    • Protein or peptide: 39S ribosomal protein L2, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L3, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L4, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L9, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L10, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L11, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L13, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L14, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L15, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L16, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L17, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L18, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L19, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L20, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L21, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L22, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L23, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L24, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L27, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L28, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L47, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L30, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L42, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L43, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L44, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L45, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L46, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L48, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L49, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L50, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L51, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L52, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L53, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L54, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein L55, mitochondrialRibosome
    • Protein or peptide: Ribosomal protein 63, mitochondrialRibosome
    • Protein or peptide: Peptidyl-tRNA hydrolase ICT1, mitochondrial
    • Protein or peptide: Growth arrest and DNA damage-inducible proteins-interacting protein 1
    • Protein or peptide: 39S ribosomal protein S18a, mitochondrialRibosome
    • Protein or peptide: 39S ribosomal protein S30, mitochondrialRibosome
    • Protein or peptide: Mitochondrial assembly of ribosomal large subunit protein 1
    • Protein or peptide: MIEF1 upstream open reading frame protein
    • Protein or peptide: Acyl carrier protein, mitochondrial
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate

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Supramolecule #1: Human mitochondrial ribosome large subunit assembly intermediate ...

SupramoleculeName: Human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#56
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293-Flp-In T-Rex / Organelle: Mitochondria

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Macromolecule #1: 39S ribosomal protein L32, mitochondrial

MacromoleculeName: 39S ribosomal protein L32, mitochondrial / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 21.437799 KDa
SequenceString:

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Macromolecule #2: 39S ribosomal protein L33, mitochondrial

MacromoleculeName: 39S ribosomal protein L33, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 7.635204 KDa
SequenceString:

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Macromolecule #3: 39S ribosomal protein L34, mitochondrial

MacromoleculeName: 39S ribosomal protein L34, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 10.183913 KDa
SequenceString:

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Macromolecule #4: 39S ribosomal protein L35, mitochondrial

MacromoleculeName: 39S ribosomal protein L35, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 21.558488 KDa
SequenceString:

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Macromolecule #5: 39S ribosomal protein L36, mitochondrial

MacromoleculeName: 39S ribosomal protein L36, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 11.809301 KDa
SequenceString:

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Macromolecule #6: 39S ribosomal protein L37, mitochondrial

MacromoleculeName: 39S ribosomal protein L37, mitochondrial / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 48.183344 KDa
SequenceString:

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Macromolecule #7: 39S ribosomal protein L38, mitochondrial

MacromoleculeName: 39S ribosomal protein L38, mitochondrial / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 44.65943 KDa
SequenceString:

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Macromolecule #8: 39S ribosomal protein L39, mitochondrial

MacromoleculeName: 39S ribosomal protein L39, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 38.764785 KDa
SequenceString:

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Macromolecule #9: 39S ribosomal protein L40, mitochondrial

MacromoleculeName: 39S ribosomal protein L40, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 24.534422 KDa
SequenceString:

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Macromolecule #10: 39S ribosomal protein L41, mitochondrial

MacromoleculeName: 39S ribosomal protein L41, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.404708 KDa
SequenceString:

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Macromolecule #13: Putative GTP-binding protein 6

MacromoleculeName: Putative GTP-binding protein 6 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.984414 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (unknown)
SequenceString:

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Macromolecule #14: 39S ribosomal protein L2, mitochondrial

MacromoleculeName: 39S ribosomal protein L2, mitochondrial / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.355941 KDa
SequenceString:

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Macromolecule #15: 39S ribosomal protein L3, mitochondrial

MacromoleculeName: 39S ribosomal protein L3, mitochondrial / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 38.689562 KDa
SequenceString:

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Macromolecule #16: 39S ribosomal protein L4, mitochondrial

MacromoleculeName: 39S ribosomal protein L4, mitochondrial / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 34.970195 KDa
SequenceString:

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Macromolecule #17: 39S ribosomal protein L9, mitochondrial

MacromoleculeName: 39S ribosomal protein L9, mitochondrial / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 30.296355 KDa
SequenceString:

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Macromolecule #18: 39S ribosomal protein L10, mitochondrial

MacromoleculeName: 39S ribosomal protein L10, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 29.322529 KDa
SequenceString:

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Macromolecule #19: 39S ribosomal protein L11, mitochondrial

MacromoleculeName: 39S ribosomal protein L11, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 20.716227 KDa
SequenceString:

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Macromolecule #20: 39S ribosomal protein L13, mitochondrial

MacromoleculeName: 39S ribosomal protein L13, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 20.722988 KDa
SequenceString:

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Macromolecule #21: 39S ribosomal protein L14, mitochondrial

MacromoleculeName: 39S ribosomal protein L14, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.973702 KDa
SequenceString:

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Macromolecule #22: 39S ribosomal protein L15, mitochondrial

MacromoleculeName: 39S ribosomal protein L15, mitochondrial / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.47382 KDa
SequenceString:

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Macromolecule #23: 39S ribosomal protein L16, mitochondrial

MacromoleculeName: 39S ribosomal protein L16, mitochondrial / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 28.496285 KDa
SequenceString:

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Macromolecule #24: 39S ribosomal protein L17, mitochondrial

MacromoleculeName: 39S ribosomal protein L17, mitochondrial / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 20.083266 KDa
SequenceString:

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Macromolecule #25: 39S ribosomal protein L18, mitochondrial

MacromoleculeName: 39S ribosomal protein L18, mitochondrial / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 20.60757 KDa
SequenceString:

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Macromolecule #26: 39S ribosomal protein L19, mitochondrial

MacromoleculeName: 39S ribosomal protein L19, mitochondrial / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 33.584996 KDa
SequenceString:

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Macromolecule #27: 39S ribosomal protein L20, mitochondrial

MacromoleculeName: 39S ribosomal protein L20, mitochondrial / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.479654 KDa
SequenceString:

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Macromolecule #28: 39S ribosomal protein L21, mitochondrial

MacromoleculeName: 39S ribosomal protein L21, mitochondrial / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.847682 KDa
SequenceString:

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Macromolecule #29: 39S ribosomal protein L22, mitochondrial

MacromoleculeName: 39S ribosomal protein L22, mitochondrial / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 23.683732 KDa
SequenceString:

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Macromolecule #30: 39S ribosomal protein L23, mitochondrial

MacromoleculeName: 39S ribosomal protein L23, mitochondrial / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.807189 KDa
SequenceString:

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Macromolecule #31: 39S ribosomal protein L24, mitochondrial

MacromoleculeName: 39S ribosomal protein L24, mitochondrial / type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 24.953875 KDa
SequenceString:

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Macromolecule #32: 39S ribosomal protein L27, mitochondrial

MacromoleculeName: 39S ribosomal protein L27, mitochondrial / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.102859 KDa
SequenceString:

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Macromolecule #33: 39S ribosomal protein L28, mitochondrial

MacromoleculeName: 39S ribosomal protein L28, mitochondrial / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 30.202867 KDa
SequenceString:

+
Macromolecule #34: 39S ribosomal protein L47, mitochondrial

MacromoleculeName: 39S ribosomal protein L47, mitochondrial / type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 29.508535 KDa
SequenceString:

+
Macromolecule #35: 39S ribosomal protein L30, mitochondrial

MacromoleculeName: 39S ribosomal protein L30, mitochondrial / type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 18.582812 KDa
SequenceString:

+
Macromolecule #36: 39S ribosomal protein L42, mitochondrial

MacromoleculeName: 39S ribosomal protein L42, mitochondrial / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 16.691176 KDa
SequenceString:

+
Macromolecule #37: 39S ribosomal protein L43, mitochondrial

MacromoleculeName: 39S ribosomal protein L43, mitochondrial / type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 23.457789 KDa
SequenceString:

+
Macromolecule #38: 39S ribosomal protein L44, mitochondrial

MacromoleculeName: 39S ribosomal protein L44, mitochondrial / type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 37.583312 KDa
SequenceString:

+
Macromolecule #39: 39S ribosomal protein L45, mitochondrial

MacromoleculeName: 39S ribosomal protein L45, mitochondrial / type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 35.402918 KDa
SequenceString:

+
Macromolecule #40: 39S ribosomal protein L46, mitochondrial

MacromoleculeName: 39S ribosomal protein L46, mitochondrial / type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 31.748107 KDa
SequenceString:

+
Macromolecule #41: 39S ribosomal protein L48, mitochondrial

MacromoleculeName: 39S ribosomal protein L48, mitochondrial / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 23.970814 KDa
SequenceString:

+
Macromolecule #42: 39S ribosomal protein L49, mitochondrial

MacromoleculeName: 39S ribosomal protein L49, mitochondrial / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 19.225043 KDa
SequenceString:

+
Macromolecule #43: 39S ribosomal protein L50, mitochondrial

MacromoleculeName: 39S ribosomal protein L50, mitochondrial / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 18.349943 KDa
SequenceString:

+
Macromolecule #44: 39S ribosomal protein L51, mitochondrial

MacromoleculeName: 39S ribosomal protein L51, mitochondrial / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.125917 KDa
SequenceString:

+
Macromolecule #45: 39S ribosomal protein L52, mitochondrial

MacromoleculeName: 39S ribosomal protein L52, mitochondrial / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 13.682658 KDa
SequenceString:

+
Macromolecule #46: 39S ribosomal protein L53, mitochondrial

MacromoleculeName: 39S ribosomal protein L53, mitochondrial / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 12.125859 KDa
SequenceString:

+
Macromolecule #47: 39S ribosomal protein L54, mitochondrial

MacromoleculeName: 39S ribosomal protein L54, mitochondrial / type: protein_or_peptide / ID: 47 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.844178 KDa
SequenceString:

+
Macromolecule #48: 39S ribosomal protein L55, mitochondrial

MacromoleculeName: 39S ribosomal protein L55, mitochondrial / type: protein_or_peptide / ID: 48 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.160433 KDa
SequenceString:

+
Macromolecule #49: Ribosomal protein 63, mitochondrial

MacromoleculeName: Ribosomal protein 63, mitochondrial / type: protein_or_peptide / ID: 49 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 12.292333 KDa
SequenceString:

+
Macromolecule #50: Peptidyl-tRNA hydrolase ICT1, mitochondrial

MacromoleculeName: Peptidyl-tRNA hydrolase ICT1, mitochondrial / type: protein_or_peptide / ID: 50 / Number of copies: 1 / Enantiomer: LEVO / EC number: aminoacyl-tRNA hydrolase
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 23.674203 KDa
SequenceString:

+
Macromolecule #51: Growth arrest and DNA damage-inducible proteins-interacting protein 1

MacromoleculeName: Growth arrest and DNA damage-inducible proteins-interacting protein 1
type: protein_or_peptide / ID: 51 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 25.426895 KDa
SequenceString:

+
Macromolecule #52: 39S ribosomal protein S18a, mitochondrial

MacromoleculeName: 39S ribosomal protein S18a, mitochondrial / type: protein_or_peptide / ID: 52 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 22.224078 KDa
SequenceString:

+
Macromolecule #53: 39S ribosomal protein S30, mitochondrial

MacromoleculeName: 39S ribosomal protein S30, mitochondrial / type: protein_or_peptide / ID: 53 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 50.429578 KDa
SequenceString:

+
Macromolecule #54: Mitochondrial assembly of ribosomal large subunit protein 1

MacromoleculeName: Mitochondrial assembly of ribosomal large subunit protein 1
type: protein_or_peptide / ID: 54 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 26.203076 KDa
SequenceString:

+
Macromolecule #55: MIEF1 upstream open reading frame protein

MacromoleculeName: MIEF1 upstream open reading frame protein / type: protein_or_peptide / ID: 55 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 8.460787 KDa
SequenceString:

+
Macromolecule #56: Acyl carrier protein, mitochondrial

MacromoleculeName: Acyl carrier protein, mitochondrial / type: protein_or_peptide / ID: 56 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 17.434273 KDa
SequenceString:

+
Macromolecule #11: 16S ribosomal RNA

MacromoleculeName: 16S ribosomal RNA / type: rna / ID: 11 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293-Flp-In T-Rex
Molecular weightTheoretical: 500.061656 KDa
SequenceString:

+
Macromolecule #12: mitochondrial tRNAVal

MacromoleculeName: mitochondrial tRNAVal / type: rna / ID: 12 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.022131 KDa
SequenceString:

+
Macromolecule #57: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 57 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #58: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 58 / Number of copies: 85 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #59: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 59 / Number of copies: 3 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.25 nm
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.1 µm / Calibrated defocus min: 0.3 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 37.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 2983982
CTF correctionSoftware - Name: Warp
Startup modelType of model: INSILICO MODEL / In silico model: ab initio
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 109894
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5ool

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7of2:
Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6.

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