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- EMDB-3842: Structure of a native assembly intermediate of the human mitochon... -

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Basic information

Entry
Database: EMDB / ID: 3842
TitleStructure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA
SampleMitochondrial ribosome large subunit with assembly factor
SourceHomo sapiens / human
Map data
Methodsingle particle reconstruction, at 3.06 Å resolution
AuthorsBrown A / Rathore S
CitationNat. Struct. Mol. Biol., 2017, 24, 866-869

Nat. Struct. Mol. Biol., 2017, 24, 866-869 Yorodumi Papers
Structures of the human mitochondrial ribosome in native states of assembly.
Alan Brown / Sorbhi Rathore / Dari Kimanius / Shintaro Aibara / Xiao-Chen Bai / Joanna Rorbach / Alexey Amunts / V Ramakrishnan

Validation ReportPDB-ID: 5ool

SummaryFull reportAbout validation report
DateDeposition: Aug 8, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Oct 18, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0853
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.0853
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5ool
  • Surface level: 0.0853
  • Imaged by UCSF CHIMERA
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Map

Fileemd_3842.map.gz (map file in CCP4 format, 174457 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
352 pix
1.06 Å/pix.
= 373.12 Å
352 pix
1.06 Å/pix.
= 373.12 Å
352 pix
1.06 Å/pix.
= 373.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.0853 (by author), 0.0853 (movie #1):
Minimum - Maximum-0.15056416 - 0.34948915
Average (Standard dev.)0.0022252756 (0.014778437)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions352352352
Origin000
Limit351351351
Spacing352352352
CellA=B=C: 373.12 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z373.120373.120373.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.1510.3490.002

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Supplemental data

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Mask #1

Fileemd_3842_msk_1.map ( map file in CCP4 format, 174457 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3842_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Mitochondrial ribosome large subunit with assembly factor

EntireName: Mitochondrial ribosome large subunit with assembly factor
Number of components: 60

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Component #1: cellular-component, Mitochondrial ribosome large subunit with ass...

Cellular-componentName: Mitochondrial ribosome large subunit with assembly factor
Recombinant expression: No
SourceSpecies: Homo sapiens / human

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Component #2: nucleic-acid, 16S ribosomal RNA

Nucleic-acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
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: Homo sapiens / human

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Component #3: nucleic-acid, mitochondrial tRNAVal

Nucleic-acidName: mitochondrial tRNAVal / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CAGAGUGUAG CUUAACACAA AGCACCCAAC UUACACUUAG GAGAUUUCAA CUUAACUUGA CCGCUCUGA
MassTheoretical: 22.022131 kDa
SourceSpecies: Homo sapiens / human

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Component #4: protein, 39S ribosomal protein L2, mitochondrial

ProteinName: 39S ribosomal protein L2, mitochondrial / Recombinant expression: No
MassTheoretical: 33.355941 kDa
SourceSpecies: Homo sapiens / human

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Component #5: protein, 39S ribosomal protein L3, mitochondrial

ProteinName: 39S ribosomal protein L3, mitochondrial / Recombinant expression: No
MassTheoretical: 38.689562 kDa
SourceSpecies: Homo sapiens / human

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Component #6: protein, 39S ribosomal protein L4, mitochondrial

ProteinName: 39S ribosomal protein L4, mitochondrial / Recombinant expression: No
MassTheoretical: 34.970195 kDa
SourceSpecies: Homo sapiens / human

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Component #7: protein, 39S ribosomal protein L9, mitochondrial

ProteinName: 39S ribosomal protein L9, mitochondrial / Recombinant expression: No
MassTheoretical: 30.296355 kDa
SourceSpecies: Homo sapiens / human

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Component #8: protein, 39S ribosomal protein L10, mitochondrial

ProteinName: 39S ribosomal protein L10, mitochondrial / Recombinant expression: No
MassTheoretical: 29.322529 kDa
SourceSpecies: Homo sapiens / human

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Component #9: protein, 39S ribosomal protein L11, mitochondrial

ProteinName: 39S ribosomal protein L11, mitochondrial / Recombinant expression: No
MassTheoretical: 20.716227 kDa
SourceSpecies: Homo sapiens / human

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Component #10: protein, 39S ribosomal protein L13, mitochondrial

ProteinName: 39S ribosomal protein L13, mitochondrial / Recombinant expression: No
MassTheoretical: 20.722988 kDa
SourceSpecies: Homo sapiens / human

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Component #11: protein, 39S ribosomal protein L14, mitochondrial

ProteinName: 39S ribosomal protein L14, mitochondrial / Recombinant expression: No
MassTheoretical: 15.973702 kDa
SourceSpecies: Homo sapiens / human

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Component #12: protein, 39S ribosomal protein L15, mitochondrial

ProteinName: 39S ribosomal protein L15, mitochondrial / Recombinant expression: No
MassTheoretical: 33.47382 kDa
SourceSpecies: Homo sapiens / human

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Component #13: protein, 39S ribosomal protein L16, mitochondrial

ProteinName: 39S ribosomal protein L16, mitochondrial / Recombinant expression: No
MassTheoretical: 28.496285 kDa
SourceSpecies: Homo sapiens / human

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Component #14: protein, 39S ribosomal protein L17, mitochondrial

ProteinName: 39S ribosomal protein L17, mitochondrial / Recombinant expression: No
MassTheoretical: 20.083266 kDa
SourceSpecies: Homo sapiens / human

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Component #15: protein, 39S ribosomal protein L18, mitochondrial

ProteinName: 39S ribosomal protein L18, mitochondrial / Recombinant expression: No
MassTheoretical: 20.60757 kDa
SourceSpecies: Homo sapiens / human

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Component #16: protein, 39S ribosomal protein L19, mitochondrial

ProteinName: 39S ribosomal protein L19, mitochondrial / Recombinant expression: No
MassTheoretical: 33.584996 kDa
SourceSpecies: Homo sapiens / human

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Component #17: protein, 39S ribosomal protein L20, mitochondrial

ProteinName: 39S ribosomal protein L20, mitochondrial / Recombinant expression: No
MassTheoretical: 17.479654 kDa
SourceSpecies: Homo sapiens / human

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Component #18: protein, 39S ribosomal protein L21, mitochondrial

ProteinName: 39S ribosomal protein L21, mitochondrial / Recombinant expression: No
MassTheoretical: 22.847682 kDa
SourceSpecies: Homo sapiens / human

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Component #19: protein, 39S ribosomal protein L22, mitochondrial

ProteinName: 39S ribosomal protein L22, mitochondrial / Recombinant expression: No
MassTheoretical: 23.683732 kDa
SourceSpecies: Homo sapiens / human

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Component #20: protein, 39S ribosomal protein L23, mitochondrial

ProteinName: 39S ribosomal protein L23, mitochondrial / Recombinant expression: No
MassTheoretical: 17.807189 kDa
SourceSpecies: Homo sapiens / human

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Component #21: protein, 39S ribosomal protein L24, mitochondrial

ProteinName: 39S ribosomal protein L24, mitochondrial / Recombinant expression: No
MassTheoretical: 24.953875 kDa
SourceSpecies: Homo sapiens / human

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Component #22: protein, 39S ribosomal protein L27, mitochondrial

ProteinName: 39S ribosomal protein L27, mitochondrial / Recombinant expression: No
MassTheoretical: 16.102859 kDa
SourceSpecies: Homo sapiens / human

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Component #23: protein, 39S ribosomal protein L28, mitochondrial

ProteinName: 39S ribosomal protein L28, mitochondrial / Recombinant expression: No
MassTheoretical: 30.202867 kDa
SourceSpecies: Homo sapiens / human

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Component #24: protein, 39S ribosomal protein L47, mitochondrial

ProteinName: 39S ribosomal protein L47, mitochondrial / Recombinant expression: No
MassTheoretical: 29.508535 kDa
SourceSpecies: Homo sapiens / human

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Component #25: protein, 39S ribosomal protein L30, mitochondrial

ProteinName: 39S ribosomal protein L30, mitochondrial / Recombinant expression: No
MassTheoretical: 18.582812 kDa
SourceSpecies: Homo sapiens / human

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Component #26: protein, 39S ribosomal protein L32, mitochondrial

ProteinName: 39S ribosomal protein L32, mitochondrial / Recombinant expression: No
MassTheoretical: 21.437799 kDa
SourceSpecies: Homo sapiens / human

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Component #27: protein, 39S ribosomal protein L33, mitochondrial

ProteinName: 39S ribosomal protein L33, mitochondrial / Recombinant expression: No
MassTheoretical: 7.635204 kDa
SourceSpecies: Homo sapiens / human

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Component #28: protein, 39S ribosomal protein L34, mitochondrial

ProteinName: 39S ribosomal protein L34, mitochondrial / Recombinant expression: No
MassTheoretical: 10.183913 kDa
SourceSpecies: Homo sapiens / human

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Component #29: protein, 39S ribosomal protein L35, mitochondrial

ProteinName: 39S ribosomal protein L35, mitochondrial / Recombinant expression: No
MassTheoretical: 21.558488 kDa
SourceSpecies: Homo sapiens / human

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Component #30: protein, 39S ribosomal protein L36, mitochondrial

ProteinName: 39S ribosomal protein L36, mitochondrial / Recombinant expression: No
MassTheoretical: 11.809301 kDa
SourceSpecies: Homo sapiens / human

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Component #31: protein, 39S ribosomal protein L37, mitochondrial

ProteinName: 39S ribosomal protein L37, mitochondrial / Recombinant expression: No
MassTheoretical: 48.183344 kDa
SourceSpecies: Homo sapiens / human

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Component #32: protein, 39S ribosomal protein L38, mitochondrial

ProteinName: 39S ribosomal protein L38, mitochondrial / Recombinant expression: No
MassTheoretical: 44.65943 kDa
SourceSpecies: Homo sapiens / human

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Component #33: protein, 39S ribosomal protein L39, mitochondrial

ProteinName: 39S ribosomal protein L39, mitochondrial / Recombinant expression: No
MassTheoretical: 38.764785 kDa
SourceSpecies: Homo sapiens / human

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Component #34: protein, 39S ribosomal protein L40, mitochondrial

ProteinName: 39S ribosomal protein L40, mitochondrial / Recombinant expression: No
MassTheoretical: 24.534422 kDa
SourceSpecies: Homo sapiens / human

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Component #35: protein, 39S ribosomal protein L41, mitochondrial

ProteinName: 39S ribosomal protein L41, mitochondrial / Recombinant expression: No
MassTheoretical: 15.404708 kDa
SourceSpecies: Homo sapiens / human

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Component #36: protein, 39S ribosomal protein L42, mitochondrial

ProteinName: 39S ribosomal protein L42, mitochondrial / Recombinant expression: No
MassTheoretical: 16.691176 kDa
SourceSpecies: Homo sapiens / human

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Component #37: protein, 39S ribosomal protein L43, mitochondrial

ProteinName: 39S ribosomal protein L43, mitochondrial / Recombinant expression: No
MassTheoretical: 23.457789 kDa
SourceSpecies: Homo sapiens / human

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Component #38: protein, 39S ribosomal protein L44, mitochondrial

ProteinName: 39S ribosomal protein L44, mitochondrial / Recombinant expression: No
MassTheoretical: 37.583312 kDa
SourceSpecies: Homo sapiens / human

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

ProteinName: 39S ribosomal protein L45, mitochondrial / Recombinant expression: No
MassTheoretical: 35.402918 kDa
SourceSpecies: Homo sapiens / human

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Component #40: protein, 39S ribosomal protein L46, mitochondrial

ProteinName: 39S ribosomal protein L46, mitochondrial / Recombinant expression: No
MassTheoretical: 31.748107 kDa
SourceSpecies: Homo sapiens / human

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Component #41: protein, 39S ribosomal protein L48, mitochondrial

ProteinName: 39S ribosomal protein L48, mitochondrial / Recombinant expression: No
MassTheoretical: 23.970814 kDa
SourceSpecies: Homo sapiens / human

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Component #42: protein, 39S ribosomal protein L49, mitochondrial

ProteinName: 39S ribosomal protein L49, mitochondrial / Recombinant expression: No
MassTheoretical: 19.225043 kDa
SourceSpecies: Homo sapiens / human

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Component #43: protein, 39S ribosomal protein L50, mitochondrial

ProteinName: 39S ribosomal protein L50, mitochondrial / Recombinant expression: No
MassTheoretical: 18.349943 kDa
SourceSpecies: Homo sapiens / human

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Component #44: protein, 39S ribosomal protein L51, mitochondrial

ProteinName: 39S ribosomal protein L51, mitochondrial / Recombinant expression: No
MassTheoretical: 15.125917 kDa
SourceSpecies: Homo sapiens / human

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Component #45: protein, 39S ribosomal protein L52, mitochondrial

ProteinName: 39S ribosomal protein L52, mitochondrial / Recombinant expression: No
MassTheoretical: 13.682658 kDa
SourceSpecies: Homo sapiens / human

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Component #46: protein, 39S ribosomal protein L53, mitochondrial

ProteinName: 39S ribosomal protein L53, mitochondrial / Recombinant expression: No
MassTheoretical: 12.125859 kDa
SourceSpecies: Homo sapiens / human

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Component #47: protein, 39S ribosomal protein L54, mitochondrial

ProteinName: 39S ribosomal protein L54, mitochondrial / Recombinant expression: No
MassTheoretical: 15.844178 kDa
SourceSpecies: Homo sapiens / human

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Component #48: protein, 39S ribosomal protein L55, mitochondrial

ProteinName: 39S ribosomal protein L55, mitochondrial / Recombinant expression: No
MassTheoretical: 15.160433 kDa
SourceSpecies: Homo sapiens / human

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Component #49: protein, Ribosomal protein 63, mitochondrial

ProteinName: Ribosomal protein 63, mitochondrial / Recombinant expression: No
MassTheoretical: 12.292333 kDa
SourceSpecies: Homo sapiens / human

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Component #50: protein, Peptidyl-tRNA hydrolase ICT1, mitochondrial

ProteinName: Peptidyl-tRNA hydrolase ICT1, mitochondrial / Recombinant expression: No
MassTheoretical: 23.674203 kDa
SourceSpecies: Homo sapiens / human

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Component #51: protein, Growth arrest and DNA damage-inducible proteins-interact...

ProteinName: Growth arrest and DNA damage-inducible proteins-interacting protein 1
Recombinant expression: No
MassTheoretical: 25.426895 kDa
SourceSpecies: Homo sapiens / human

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Component #52: protein, 39S ribosomal protein S18a, mitochondrial

ProteinName: 39S ribosomal protein S18a, mitochondrial / Recombinant expression: No
MassTheoretical: 22.224078 kDa
SourceSpecies: Homo sapiens / human

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Component #53: protein, 39S ribosomal protein S30, mitochondrial

ProteinName: 39S ribosomal protein S30, mitochondrial / Recombinant expression: No
MassTheoretical: 50.429578 kDa
SourceSpecies: Homo sapiens / human

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Component #54: protein, Unknown protein or protein extension

ProteinName: Unknown protein or protein extension / Recombinant expression: No
MassTheoretical: 2.400951 kDa
SourceSpecies: Homo sapiens / human

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Component #55: protein, Mitochondrial assembly of ribosomal large subunit protein 1

ProteinName: Mitochondrial assembly of ribosomal large subunit protein 1
Recombinant expression: No
MassTheoretical: 26.203076 kDa
SourceSpecies: Homo sapiens / human

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Component #56: protein, MIEF1 upstream open reading frame protein

ProteinName: MIEF1 upstream open reading frame protein / Recombinant expression: No
MassTheoretical: 8.460787 kDa
SourceSpecies: Homo sapiens / human

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Component #57: protein, Acyl carrier protein, mitochondrial

ProteinName: Acyl carrier protein, mitochondrial / Recombinant expression: No
MassTheoretical: 17.434273 kDa
SourceSpecies: Homo sapiens / human

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Component #58: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 92 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #59: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #60: ligand, 4'-PHOSPHOPANTETHEINE

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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation.
pH: 7.45
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Details: Sample incubated for 30 s prior to freezing.

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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: 1.56 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130841 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 134685
3D reconstructionSoftware: RELION / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: Cross-correlation coefficient / Refinement space: REAL
Input PDB model: 3J9M
Overall bvalue: 85
Output model

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