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- EMDB-12921: Cryo-EM structure of late human 39S mitoribosome assembly interme... -

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Basic information

Entry
Database: EMDB / ID: EMD-12921
TitleCryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3A
Map data
SampleHuman 39S mitoribosome assembly intermediates, state 3A
  • (39S ribosomal protein ...) x 46
  • Ribosomal protein 63, mitochondrialRibosome
  • Peptidyl-tRNA hydrolase ICT1, mitochondrial
  • Growth arrest and DNA damage-inducible proteins-interacting protein 1
  • Mitochondrial assembly of ribosomal large subunit protein 1
  • MIEF1 upstream open reading frame protein
  • Acyl carrier protein, mitochondrial
  • (nucleic-acidNucleic acid) x 3
  • (ligand) x 3
Function / homology
Function and homology information


negative regulation of mitochondrial translation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / negative regulation of ribosome biogenesis / rRNA import into mitochondrion / Respiratory electron transport / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial translational termination ...negative regulation of mitochondrial translation / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / negative regulation of ribosome biogenesis / rRNA import into mitochondrion / Respiratory electron transport / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial translational termination / positive regulation of mitochondrial translation / translation release factor activity, codon nonspecific / mitochondrial translational elongation / mitochondrial ribosome / mitochondrial small ribosomal subunit / protein lipoylation / mitochondrial respiratory chain complex I / acyl binding / aminoacyl-tRNA hydrolase / Glyoxylate metabolism and glycine degradation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / aminoacyl-tRNA hydrolase activity / ribonuclease III activity / mitochondrial translation / primary miRNA processing / production of siRNA involved in RNA interference / pre-miRNA processing / mitochondrial large ribosomal subunit / ribosomal large subunit binding / regulation of cell cycle => GO:0051726 / RNA processing / anatomical structure morphogenesis / ribosomal large subunit biogenesis / fatty acid binding / cellular response to leukemia inhibitory factor / mitochondrial membrane / ribosome assembly / fibrillar center / small ribosomal subunit rRNA binding / large ribosomal subunit rRNA binding / fatty acid biosynthetic process / large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / double-stranded RNA binding / ribosome biogenesis / ribonucleoprotein complex / cell junction / mitochondrial inner membrane / nuclear membrane / negative regulation of translation / ribosome / rRNA binding / nuclear body / structural constituent of ribosome / cell cycle / hydrolase activity / mitochondrial matrix / translation / mRNA binding / protein domain specific binding / nucleotide binding / apoptotic process / nucleolus / calcium ion binding / viral process / mitochondrion / RNA binding / extracellular space / nucleoplasm / plasma membrane / nucleus / cytosol
Similarity search - Function
Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Mitochondrial ribosomal subunit / Mitochondrial ribosomal protein L48 / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily ...Protein Iojap/ribosomal silencing factor RsfS / Ribosomal protein S30, mitochondrial / Ribosomal protein L55, mitochondrial / Mitochondrial ribosomal protein L55 / Ribosomal protein L51, mitochondrial / Mitochondrial 28S ribosomal protein S32 / Mitochondrial ribosomal subunit / Mitochondrial ribosomal protein L48 / Mitochondrial ribosome protein 63 / Growth arrest and DNA damage-inducible proteins-interacting protein 1 domain superfamily / Ribosomal protein 63, mitochondrial / Mitochondrial 28S ribosomal protein S30 (PDCD9) / Growth arrest and DNA-damage-inducible proteins-interacting protein 1 / Ribosomal protein L37/S30 / Ribosomal protein L37, mitochondrial / Growth arrest/ DNA-damage-inducible protein-interacting protein 1 / Mitochondrial ribosomal protein L37 / 39S ribosomal protein L42, mitochondrial / 39S ribosomal protein L40, mitochondrial / Mitochondrial ribosomal protein L46 NUDIX / Mitoribosomal protein mL52 / Ribosomal protein L53, mitochondrial / 39S ribosomal protein L52, mitochondrial / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L53/MRP-L53 / Tim44 / Tim44-like domain / Tim44-like domain / Mitochondrial ribosomal protein L28 / MRPL44, double-stranded RNA binding domain / Ribosomal protein L28/L40, mitochondrial / Ribosomal protein L49/IMG2 / Mitochondrial large subunit ribosomal protein (Img2) / Ribosomal protein L50, mitochondria / Ribosomal protein L27/L41, mitochondrial / Mitochondrial ribosomal protein L27 / Ribosomal subunit 39S / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / 39S ribosomal protein L46, mitochondrial / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / MRP-L47 superfamily, mitochondrial / Ribosomal protein L47, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / TGS domain profile. / TGS / TGS-like / Complex 1 protein (LYR family) / Complex 1 LYR protein / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / Ribonuclease III, endonuclease domain superfamily / Peptide chain release factor class I / RF-1 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Beta-grasp domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / NTF2-like domain superfamily / Ribosomal protein L11, bacterial-type / Ribosomal protein L10-like domain superfamily / Phosphopantetheine attachment site / Ribosomal protein L10 / Ribosomal protein L10P / NUDIX hydrolase-like domain superfamily / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Ribosomal protein L28/L24 superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, C-terminal / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Nucleotidyltransferase superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L35 / Ribosomal protein L33 superfamily / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Similarity search - Domain/homology
39S ribosomal protein L9, mitochondrial / 39S ribosomal protein L18, mitochondrial / 39S ribosomal protein L37, mitochondrial / 39S ribosomal protein L4, mitochondrial / Ribosomal protein 63, mitochondrial / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L20, mitochondrial / 39S ribosomal protein L32, mitochondrial / 39S ribosomal protein L45, mitochondrial / 39S ribosomal protein L44, mitochondrial ...39S ribosomal protein L9, mitochondrial / 39S ribosomal protein L18, mitochondrial / 39S ribosomal protein L37, mitochondrial / 39S ribosomal protein L4, mitochondrial / Ribosomal protein 63, mitochondrial / 39S ribosomal protein L13, mitochondrial / 39S ribosomal protein L20, mitochondrial / 39S ribosomal protein L32, mitochondrial / 39S ribosomal protein L45, mitochondrial / 39S ribosomal protein L44, mitochondrial / 39S ribosomal protein L46, mitochondrial / 39S ribosomal protein S18a, mitochondrial / 39S ribosomal protein L47, mitochondrial / 39S ribosomal protein S30, mitochondrial / 39S ribosomal protein L40, mitochondrial / 39S ribosomal protein L17, mitochondrial / 39S ribosomal protein L48, 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 L27, mitochondrial / 39S ribosomal protein L11, mitochondrial / 39S ribosomal protein L34, mitochondrial / Growth arrest and DNA damage-inducible proteins-interacting protein 1 / 39S ribosomal protein L53, mitochondrial / 39S ribosomal protein L2, mitochondrial / MIEF1 upstream open reading frame protein / Acyl carrier protein, mitochondrial / 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 L54, mitochondrial / Mitochondrial assembly of ribosomal large subunit protein 1 / 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 / 39S ribosomal protein L30, mitochondrial / 39S ribosomal protein L24, mitochondrial / 39S ribosomal protein L38, mitochondrial / 39S ribosomal protein L42, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng J / Berninghausen O / Beckmann R
CitationJournal: Nat Commun / Year: 2021
Title: A distinct assembly pathway of the human 39S late pre-mitoribosome.
Authors: Jingdong Cheng / Otto Berninghausen / Roland Beckmann /
Abstract: Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. ...Assembly of the mitoribosome is largely enigmatic and involves numerous assembly factors. Little is known about their function and the architectural transitions of the pre-ribosomal intermediates. Here, we solve cryo-EM structures of the human 39S large subunit pre-ribosomes, representing five distinct late states. Besides the MALSU1 complex used as bait for affinity purification, we identify several assembly factors, including the DDX28 helicase, MRM3, GTPBP10 and the NSUN4-mTERF4 complex, all of which keep the 16S rRNA in immature conformations. The late transitions mainly involve rRNA domains IV and V, which form the central protuberance, the intersubunit side and the peptidyltransferase center of the 39S subunit. Unexpectedly, we find deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly. Taken together, our study provides an architectural inventory of the distinct late assembly phase of the human 39S mitoribosome.
History
DepositionMay 11, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7oi8
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12921.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 360 pix.
= 390.24 Å
1.08 Å/pix.
x 360 pix.
= 390.24 Å
1.08 Å/pix.
x 360 pix.
= 390.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.04
Minimum - Maximum-0.5382862 - 0.85364544
Average (Standard dev.)0.00053395913 (±0.020550102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 390.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z390.240390.240390.240
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.5380.8540.001

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Supplemental data

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Additional map: unfiltered map

Fileemd_12921_additional_1.map
Annotationunfiltered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Human 39S mitoribosome assembly intermediates, state 3A

EntireName: Human 39S mitoribosome assembly intermediates, state 3A
Number of Components: 59

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Component #1: protein, Human 39S mitoribosome assembly intermediates, state 3A

ProteinName: Human 39S mitoribosome assembly intermediates, state 3A
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, 39S ribosomal protein L2, mitochondrial

ProteinName: 39S ribosomal protein L2, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.355941 kDa
SourceSpecies: Human (human)

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Component #3: protein, 39S ribosomal protein L3, mitochondrial

ProteinName: 39S ribosomal protein L3, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.689562 kDa
SourceSpecies: Human (human)

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Component #4: protein, 39S ribosomal protein L4, mitochondrial

ProteinName: 39S ribosomal protein L4, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.970195 kDa
SourceSpecies: Human (human)

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Component #5: protein, 39S ribosomal protein L9, mitochondrial

ProteinName: 39S ribosomal protein L9, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.296355 kDa
SourceSpecies: Human (human)

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Component #6: protein, 39S ribosomal protein L10, mitochondrial

ProteinName: 39S ribosomal protein L10, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.322529 kDa
SourceSpecies: Human (human)

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Component #7: protein, 39S ribosomal protein L11, mitochondrial

ProteinName: 39S ribosomal protein L11, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.716227 kDa
SourceSpecies: Human (human)

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Component #8: protein, 39S ribosomal protein L13, mitochondrial

ProteinName: 39S ribosomal protein L13, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.722988 kDa
SourceSpecies: Human (human)

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Component #9: protein, 39S ribosomal protein L14, mitochondrial

ProteinName: 39S ribosomal protein L14, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.973702 kDa
SourceSpecies: Human (human)

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Component #10: protein, 39S ribosomal protein L15, mitochondrial

ProteinName: 39S ribosomal protein L15, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.47382 kDa
SourceSpecies: Human (human)

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Component #11: protein, 39S ribosomal protein L16, mitochondrial

ProteinName: 39S ribosomal protein L16, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.496285 kDa
SourceSpecies: Human (human)

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Component #12: protein, 39S ribosomal protein L17, mitochondrial

ProteinName: 39S ribosomal protein L17, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.083266 kDa
SourceSpecies: Human (human)

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Component #13: protein, 39S ribosomal protein L18, mitochondrial

ProteinName: 39S ribosomal protein L18, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.60757 kDa
SourceSpecies: Human (human)

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Component #14: protein, 39S ribosomal protein L19, mitochondrial

ProteinName: 39S ribosomal protein L19, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.584996 kDa
SourceSpecies: Human (human)

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Component #15: protein, 39S ribosomal protein L20, mitochondrial

ProteinName: 39S ribosomal protein L20, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.479654 kDa
SourceSpecies: Human (human)

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Component #16: protein, 39S ribosomal protein L21, mitochondrial

ProteinName: 39S ribosomal protein L21, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.847682 kDa
SourceSpecies: Human (human)

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Component #17: protein, 39S ribosomal protein L22, mitochondrial

ProteinName: 39S ribosomal protein L22, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.683732 kDa
SourceSpecies: Human (human)

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Component #18: protein, 39S ribosomal protein L23, mitochondrial

ProteinName: 39S ribosomal protein L23, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.807189 kDa
SourceSpecies: Human (human)

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Component #19: protein, 39S ribosomal protein L24, mitochondrial

ProteinName: 39S ribosomal protein L24, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.953875 kDa
SourceSpecies: Human (human)

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Component #20: protein, 39S ribosomal protein L27, mitochondrial

ProteinName: 39S ribosomal protein L27, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.102859 kDa
SourceSpecies: Human (human)

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Component #21: protein, 39S ribosomal protein L28, mitochondrial

ProteinName: 39S ribosomal protein L28, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.202867 kDa
SourceSpecies: Human (human)

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Component #22: protein, 39S ribosomal protein L47, mitochondrial

ProteinName: 39S ribosomal protein L47, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.508535 kDa
SourceSpecies: Human (human)

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Component #23: protein, 39S ribosomal protein L30, mitochondrial

ProteinName: 39S ribosomal protein L30, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.582812 kDa
SourceSpecies: Human (human)

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Component #24: protein, 39S ribosomal protein L32, mitochondrial

ProteinName: 39S ribosomal protein L32, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.437799 kDa
SourceSpecies: Human (human)

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Component #25: protein, 39S ribosomal protein L33, mitochondrial

ProteinName: 39S ribosomal protein L33, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.635204 kDa
SourceSpecies: Human (human)

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Component #26: protein, 39S ribosomal protein L34, mitochondrial

ProteinName: 39S ribosomal protein L34, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.183913 kDa
SourceSpecies: Human (human)

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Component #27: protein, 39S ribosomal protein L35, mitochondrial

ProteinName: 39S ribosomal protein L35, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.558488 kDa
SourceSpecies: Human (human)

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Component #28: protein, 39S ribosomal protein L37, mitochondrial

ProteinName: 39S ribosomal protein L37, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.183344 kDa
SourceSpecies: Human (human)

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Component #29: protein, 39S ribosomal protein L38, mitochondrial

ProteinName: 39S ribosomal protein L38, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.65943 kDa
SourceSpecies: Human (human)

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Component #30: protein, 39S ribosomal protein L39, mitochondrial

ProteinName: 39S ribosomal protein L39, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.764785 kDa
SourceSpecies: Human (human)

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Component #31: protein, 39S ribosomal protein L40, mitochondrial

ProteinName: 39S ribosomal protein L40, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.534422 kDa
SourceSpecies: Human (human)

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Component #32: protein, 39S ribosomal protein L41, mitochondrial

ProteinName: 39S ribosomal protein L41, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.404708 kDa
SourceSpecies: Human (human)

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Component #33: protein, 39S ribosomal protein L42, mitochondrial

ProteinName: 39S ribosomal protein L42, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.691176 kDa
SourceSpecies: Human (human)

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Component #34: protein, 39S ribosomal protein L43, mitochondrial

ProteinName: 39S ribosomal protein L43, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.457789 kDa
SourceSpecies: Human (human)

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Component #35: protein, 39S ribosomal protein L44, mitochondrial

ProteinName: 39S ribosomal protein L44, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.583312 kDa
SourceSpecies: Human (human)

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Component #36: protein, 39S ribosomal protein L45, mitochondrial

ProteinName: 39S ribosomal protein L45, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.402918 kDa
SourceSpecies: Human (human)

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Component #37: protein, 39S ribosomal protein L46, mitochondrial

ProteinName: 39S ribosomal protein L46, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.748107 kDa
SourceSpecies: Human (human)

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Component #38: protein, 39S ribosomal protein L48, mitochondrial

ProteinName: 39S ribosomal protein L48, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.970814 kDa
SourceSpecies: Human (human)

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Component #39: protein, 39S ribosomal protein L49, mitochondrial

ProteinName: 39S ribosomal protein L49, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.225043 kDa
SourceSpecies: Human (human)

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Component #40: protein, 39S ribosomal protein L50, mitochondrial

ProteinName: 39S ribosomal protein L50, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.349943 kDa
SourceSpecies: Human (human)

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Component #41: protein, 39S ribosomal protein L51, mitochondrial

ProteinName: 39S ribosomal protein L51, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.125917 kDa
SourceSpecies: Human (human)

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Component #42: protein, 39S ribosomal protein L52, mitochondrial

ProteinName: 39S ribosomal protein L52, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.682658 kDa
SourceSpecies: Human (human)

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Component #43: protein, 39S ribosomal protein L53, mitochondrial

ProteinName: 39S ribosomal protein L53, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.125859 kDa
SourceSpecies: Human (human)

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Component #44: protein, 39S ribosomal protein L54, mitochondrial

ProteinName: 39S ribosomal protein L54, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.844178 kDa
SourceSpecies: Human (human)

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Component #45: protein, 39S ribosomal protein L55, mitochondrial

ProteinName: 39S ribosomal protein L55, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.160433 kDa
SourceSpecies: Human (human)

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Component #46: protein, Ribosomal protein 63, mitochondrial

ProteinName: Ribosomal protein 63, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.292333 kDa
SourceSpecies: Human (human)

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Component #47: protein, Peptidyl-tRNA hydrolase ICT1, mitochondrial

ProteinName: Peptidyl-tRNA hydrolase ICT1, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.674203 kDa
SourceSpecies: Human (human)

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Component #48: protein, Growth arrest and DNA damage-inducible proteins-interact...

ProteinName: Growth arrest and DNA damage-inducible proteins-interacting protein 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.426895 kDa
SourceSpecies: Human (human)

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Component #49: protein, 39S ribosomal protein S18a, mitochondrial

ProteinName: 39S ribosomal protein S18a, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.224078 kDa
SourceSpecies: Human (human)

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Component #50: protein, 39S ribosomal protein S30, mitochondrial

ProteinName: 39S ribosomal protein S30, mitochondrialRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.429578 kDa
SourceSpecies: Human (human)

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Component #51: protein, Mitochondrial assembly of ribosomal large subunit protein 1

ProteinName: Mitochondrial assembly of ribosomal large subunit protein 1
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.203076 kDa
SourceSpecies: Human (human)

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Component #52: protein, MIEF1 upstream open reading frame protein

ProteinName: MIEF1 upstream open reading frame protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.460787 kDa
SourceSpecies: Human (human)

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Component #53: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.434273 kDa
SourceSpecies: Human (human)

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Component #54: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GCUAAACCUA GCCCCAAACC CACUCCACCU UACUACCAGA CAACCUUAGC CAAACCAUUU ACCCAAAUAA AGUAUAGGCG AUAGAAAUUG AAACCUGGCG CAAUAGAUAU AGUACCGCAA GGGAAAGAUG AAAAAUUAUA ACCAAGCAUA AUAUAGCAAG GACUAACCCC ...Sequence:
GCUAAACCUA GCCCCAAACC CACUCCACCU UACUACCAGA CAACCUUAGC CAAACCAUUU ACCCAAAUAA AGUAUAGGCG AUAGAAAUUG AAACCUGGCG CAAUAGAUAU AGUACCGCAA GGGAAAGAUG AAAAAUUAUA ACCAAGCAUA AUAUAGCAAG GACUAACCCC UAUACCUUCU GCAUAAUGAA UUAACUAGAA AUAACUUUGC AAGGAGAGCC AAAGCUAAGA CCCCCGAAAC CAGACGAGCU ACCUAAGAAC AGCUAAAAGA GCACACCCGU CUAUGUAGCA AAAUAGUGGG AAGAUUUAUA GGUAGAGGCG ACAAACCUAC CGAGCCUGGU GAUAGCUGGU UGUCCAAGAU AGAAUCUUAG UUCAACUUUA AAUUUGCCCA CAGAACCCUC UAAAUCCCCU UGUAAAUUUA ACUGUUAGUC CAAAGAGGAA CAGCUCUUUG GACACUAGGA AAAAACCUUG UAGAGAGAGU AAAAAAUUUA ACACCCAUAG UAGGCCUAAA AGCAGCCACC AAUUAAGAAA GCGUUCAAGC UCAACACCCA CUACCUAAAA AAUCCCAAAC AUAUAACUGA ACUCCUCACA CCCAAUUGGA CCAAUCUAUC ACCCUAUAGA AGAACUAAUG UUAGUAUAAG UAACAUGAAA ACAUUCUCCU CCGCAUAAGC CUGCGUCAGA UUAAAACACU GAACUGACAA UUAACAGCCC AAUAUCUACA AUCAACCAAC AAGUCAUUAU UACCCUCACU GUCAACCCAA CACAGGCAUG CUCAUAAGGA AAGGUUAAAA AAAGUAAAAG GAACUCGGCA AAUCUUACCC CGCCUGUUUA CCAAAAACAU CACCUCUAGC AUCACCAGUA UUAGAGGCAC CGCCUGCCCA GUGACACAUG UUUAACGGCC GCGGUACCCU AACCGUGCAA AGGUAGCAUA AUCACUUGUU CCUUAAAUAG GGACCUGUAU GAAUGGCUCC ACGAGGGUUC AGCUGUCUCU UACUUUUAAC CAGUGAAAUU GACCUGCCCG UGAAGAGGCG GGCAUAACAC AGCAAGACGA GAAGACCCUA UGGAGCUUUA AUUUAUUAAU GCAAACAGUA CCUAACAAAC CCACAGGUCC UAAACUACCA AACCUGCAUU AAAAAUUUCG GUUGGGGCGA CCUCGGAGCA GAACCCAACC UCCGAGCAGU ACAUGCUAAG ACUUCACCAG UCAAAGCGAA CUACUAUACU CAAUUGAUCC AAUAACUUGA CCAACGGAAC AAGUUACCCU AGGGAUAACA GCGCAAUCCU AUUCUAGAGU CCAUAUCAAC AAUAGGGUUU ACGACCUCGA UGUUGGAUCA GGACAUCCCG AUGGUGCAGC CGCUAUUAAA GGUUCGUUUG UUCAACGAUU AAAGUCCUAC GUGAUCUGAG UUCAGACCGG AGUAAUCCAG GUCGGUUUCU AUCUACUUUC AAAUUCCUCC CUGUACGAAA GGACAAGAGA AAUAAGGCCU ACUUCACAAA GCGCCUUCCC CCGUAAAUGA UAUCAUCUCA ACUUAGUAUU AUACCCACAC CCACCCAAGA ACAGGGUUU
MassTheoretical: 500.019594 kDa
SourceSpecies: Human (human)

+
Component #55: nucleic-acid, mitochondrial Val tRNA

nucleic acidName: mitochondrial Val tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAGAGUGUAG CUUAACACAA AGCACCCAAC UUACACUUAG GAGAUUUCAA CUUAACUUGA CCGCUCUGA
MassTheoretical: 22.022131 kDa
SourceSpecies: Human (human)

+
Component #56: nucleic-acid, mitochondrial tRNA

nucleic acidName: mitochondrial tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGUUAUGUAG CUUAAAUUAU CAAAGCAAGG CACUGAAAAU GCCUAGAUGA GCCUCACAGC UCCAUUAACA CCA
MassTheoretical: 23.378979 kDa
SourceSpecies: Human (human)

+
Component #57: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 49 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #58: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #59: ligand, 4'-PHOSPHOPANTETHEINE

LigandName: 4'-PHOSPHOPANTETHEINEPhosphopantetheine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.358348 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 28 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 59666
3D reconstructionResolution: 3.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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