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- EMDB-10223: Cryo-EM Structure of T. kodakarensis 70S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-10223
TitleCryo-EM Structure of T. kodakarensis 70S ribosome
Map data
Sample70S ribosome from Thermococcus kodakarensisRibosome
  • (nucleic-acidNucleic acid) x 3
  • (30S ribosomal protein ...) x 24
  • Predicted zinc-ribbon RNA-binding protein involved in translation
  • (50S ribosomal protein ...) x 32
  • LSU ribosomal protein L41E
  • (ligand) x 2
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly ...ribonuclease P activity / tRNA 5'-leader removal / maturation of SSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of LSU-rRNA / assembly of large subunit precursor of preribosome / positive regulation of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / ribosomal large subunit assembly / cytosolic large ribosomal subunit / 5S rRNA binding / cytosolic small ribosomal subunit / small ribosomal subunit / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / RNA binding / zinc ion binding / cytosol
Ribosomal protein L14P, archaeal / Ribosomal protein S9, conserved site / Ribosomal protein L3, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein L4 / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S17, conserved site / Ribosomal protein L23 ...Ribosomal protein L14P, archaeal / Ribosomal protein S9, conserved site / Ribosomal protein L3, archaeal / Ribosomal protein S9, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein L4 / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S17, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S8e, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein S6e, archaeal / Ribosomal protein L15e, conserved site / Ribosomal protein L15e, archaeal / Ribosomal protein S19 conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein L7Ae, archaea / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein S4/S9 / Ribosomal protein S4, archaeal / Ribosomal protein L3, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L5, archaeal / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein L2, domain 3 / K homology domain-like, alpha/beta / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein S4, conserved site / Ribosomal S24e conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein S8e, conserved site / Ribosomal protein L10e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L21e, archaeal / RNA-binding S4 domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S28e conserved site / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / 30S ribosomal protein S3Ae / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L19/L19e superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L32e superfamily / Ribosomal protein S3, archaeal / Winged helix DNA-binding domain superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein S19e, archaeal / Ribosomal protein S10 domain / Ribosomal protein S12, archaea / Ribosomal protein S19, superfamily / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L30e, conserved site / Ribosomal protein S15P / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein S27e, zinc-binding domain superfamily / Ribosomal protein L24e / Ribosomal protein L24e, conserved site
50S ribosomal protein L40e / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 50S ribosomal protein L14e / 30S ribosomal protein S9 / 50S ribosomal protein L37e / 30S ribosomal protein S2 / 30S ribosomal protein S24e / 50S ribosomal protein L21e / 50S ribosomal protein L15e ...50S ribosomal protein L40e / 30S ribosomal protein S4 / 30S ribosomal protein S13 / 50S ribosomal protein L14e / 30S ribosomal protein S9 / 50S ribosomal protein L37e / 30S ribosomal protein S2 / 30S ribosomal protein S24e / 50S ribosomal protein L21e / 50S ribosomal protein L15e / 50S ribosomal protein L18e / 30S ribosomal protein S11 / 30S ribosomal protein S14 type Z / 50S ribosomal protein L13 / 50S ribosomal protein L34e / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 30S ribosomal protein S4e / 50S ribosomal protein L5 / 50S ribosomal protein L31e / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 50S ribosomal protein L32e / 50S ribosomal protein L19e / 50S ribosomal protein L18 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 50S ribosomal protein L39e / 30S ribosomal protein S15 / 50S ribosomal protein L18Ae / 50S ribosomal protein L37Ae / 30S ribosomal protein S17e / 50S ribosomal protein L23 / 50S ribosomal protein L2 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 30S ribosomal protein S3 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L4 / 50S ribosomal protein L10e / 50S ribosomal protein L3 / 30S ribosomal protein S6e / 30S ribosomal protein S7 / 50S ribosomal protein L24e / 30S ribosomal protein S12 / 50S ribosomal protein L30e / 30S ribosomal protein S27e / 50S ribosomal protein L44e / LSU ribosomal protein L41E / Predicted zinc-ribbon RNA-binding protein involved in translation / 30S ribosomal protein S10 / 30S ribosomal protein S8e / 30S ribosomal protein S3Ae / 30S ribosomal protein S19e / 50S ribosomal protein L7Ae / 30S ribosomal protein S28e / 50S ribosomal protein L15
Biological speciesThermococcus kodakarensis (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsMatzov D / Sas-Chen A / Thomas JM / Santangelo T / Meier JL / Schwartz S / Shalev-Benami M
CitationJournal: Nature / Year: 2020
Title: Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.
Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / ...Authors: Aldema Sas-Chen / Justin M Thomas / Donna Matzov / Masato Taoka / Kellie D Nance / Ronit Nir / Keri M Bryson / Ran Shachar / Geraldy L S Liman / Brett W Burkhart / Supuni Thalalla Gamage / Yuko Nobe / Chloe A Briney / Michaella J Levy / Ryan T Fuchs / G Brett Robb / Jesse Hartmann / Sunny Sharma / Qishan Lin / Laurence Florens / Michael P Washburn / Toshiaki Isobe / Thomas J Santangelo / Moran Shalev-Benami / Jordan L Meier / Schraga Schwartz /
Abstract: N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics ...N-acetylcytidine (acC) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report acC-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of acC at single-nucleotide resolution. In human and yeast mRNAs, acC sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of acC across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. AcC is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of acC and its potential thermoadaptive role. Our studies quantitatively define the acC landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease.
Validation ReportPDB-ID: 6skf

SummaryFull reportAbout validation report
History
DepositionAug 15, 2019-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing 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
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6skf
  • 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_10223.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 408. Å
0.85 Å/pix.
x 480 pix.
= 408. Å
0.85 Å/pix.
x 480 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.04
Minimum - Maximum-0.24538869 - 0.44123247
Average (Standard dev.)0.0003702157 (±0.011424991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.2450.4410.000

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Supplemental data

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Additional map: T. kodakarensis 50S map

Fileemd_10223_additional_1.map
AnnotationT. kodakarensis 50S map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: T. kodakarensis 50S unsharpened map

Fileemd_10223_additional_2.map
AnnotationT. kodakarensis 50S unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: T. kodakarensis 30S body unsharpened map

Fileemd_10223_additional_3.map
AnnotationT. kodakarensis 30S body unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: T. kodakarensis 30S body unsharpened map

Fileemd_10223_additional_4.map
AnnotationT. kodakarensis 30S body unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: T. kodakarensis 30S head map

Fileemd_10223_additional_5.map
AnnotationT. kodakarensis 30S head map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: T. kodakarensis 30S head unsharpened map

Fileemd_10223_additional_6.map
AnnotationT. kodakarensis 30S head unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire 70S ribosome from Thermococcus kodakarensis

EntireName: 70S ribosome from Thermococcus kodakarensisRibosome / Number of components: 64

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Component #1: protein, 70S ribosome from Thermococcus kodakarensis

ProteinName: 70S ribosome from Thermococcus kodakarensisRibosome / Recombinant expression: No
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #2: nucleic-acid, 16S rRNA

nucleic acidName: 16S rRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AUUC(4AC)GG(OMU)UG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC A(OMU)GCGAGUCA UGGGGCGCGC UCUGCGCGCA CCGGCGGACG GCUCAGUAAC ACGUCGGUAA CCUACCCUCG GGAGGGGGAU AACCC(4AC)G(OMG)GA AACUGGGGCU ...Sequence:
AUUC(4AC)GG(OMU)UG AUCCUGCCGG AGGCCACUGC UAUGGGGGUC (4AC)GACUAAGCC A(OMU)GCGAGUCA UGGGGCGCGC UCUGCGCGCA CCGGCGGACG GCUCAGUAAC ACGUCGGUAA CCUACCCUCG GGAGGGGGAU AACCC(4AC)G(OMG)GA AACUGGGGCU AAUCCCCCAU AGGCCUGAGG UACUGGAAGG UCCUCAGGC(OMC) GAAAGGGGCA UCUGCCCGCC CGAGGAUGGG CCGGCGGC(LHH)G AUUAGGUAG(OMU) UGGUG(OMG)GGUA ACGGCCCACC AAGCCGAAGA UCGGUACGGG CCAUGAGAGU GGGAG(OMC)C(4AC)GG AGA(OMU)GGACAC UGAGACACG(OMG) GUCCAGGCCC UACGGGGCGC AGCAGGCGCG A(A2M)ACCUC(4AC)GC AAUGCGGGCA AC(4AC)GCGACGG (OMG)(OMG)GGACCCCC AGUGCCGUGG CAUAGCCACG GCUUUUCCGG AGUGUAAAAA GCUCCGGGAA UAAGG(OMG)CUG(OMG) GCAAGG(5MC)(4AC)GG UGG(5MC)AGCCGC CGCGGUAA(OMU)A CCGGCGGCCC GAGUGGU(OMG)GC (4AC)GCUAUUAUU GGGCCUAAAG CGUC(4AC)GUAGC C(OMG)GG(OMC)CCGUA AGUCCCUGGC GAAAUCCCAC GGCUCAAC(4AC)G UGGGGCUUGC UGGGGAUACU GCGGGCCUUG GGAC(4AC)GGGAG AGGCCGGGGG UACCCCUGGG GUAGG(OMG)GUGA AAUCCUAUAA UCCCAGGG(OMG)G ACCGCCAGU(2MG) G(5MC)GAAGGCGC C(4AC)GGCUGGAA CGGGUC(4AC)GAC GGUGAGGGAC GAAGGCCAGG GGAGCGAAC(4AC) GGAUUAGAUA CCCGGGUAGU C(OMC)UGGCUGUA AAGGAUGCGG (OMG)CUAGGUGUC GGGCGAGCUU CGAGCUCGCC CGGUGCCGGA GGGAAGC(4AC)GU UAAG(OMC)C(4AC)GCC GCCUGGGGAG UACGGC(4AC)GCA A(OMG)G(5MC)UGAAAC UUAAAGGAAU UGGCG(OMG)GGGA GCACUACAAG G(OMG)GUGGAGCG UGCGGUUUAA UU(OMG)GAU(5MU)(LV2)AA CGCCGGGAAC CUCACCGGGG G(5MC)GACGGCAG GAUGAAGGCC AGGCUGAAGG UCUUGCCGGA CACGCCGAGA GGA(OMG)GUGCAU GGC(5MC)GC(4AC)GUC AGCUCGUAC(LHH) GUGA(OMG)(OMG)CGUC CACUUAAGUG UGGUAACGAG (B8T)GAGACCCGC GCCCCCAGUU GCCAGUCCUC CCCGCUGGGG AGGAGGCACU CUGGGG(OMG)GAC CGCCGGCGAU AAGCCGGAGG AAGGAGCGGG (B8T)GACGGUAGG UCAGUAUGCC CCGAAACCCC CGGGCUACAC GCGCGCUACA AUGGGCGGGA CAAUGGGAUC CGACCC(4AC)GAA AGGGGAAGGG AAUCCCCUAA ACCCGCCCUC AGUUCGGAUC G(B8T)GG(OMG)CUGCA ACUC(OMG)(5MC)CCGC GUGAAGCUGG AAUCCCUAGU ACCCGCGUGU CAUCAUCGCG CGGCGAAUAC GUCCCUGCUC CUUGCACACA C(5MC)G(OMC)CCG(OMU)CA (OMC)UCCACCCGA GCGGGGUCCG GGUGAGGCCU GGUCUCCCUU CGGGGAGGCC GGGUCGAGCC UGGGCUCCGU GAG(OMG)GGGGAG AAGUCGUA(6MZ)C AAGGUAGC(4AC)G UAGGGG(MA6)(MA6)CC UACGG(5MC)U(5MC)GA UCACCUCCUA UCGCCGGA
MassTheoretical: 488.234531 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #3: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.039793 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #4: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.39016 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #5: protein, 30S ribosomal protein S3Ae

ProteinName: 30S ribosomal protein S3AeRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.06492 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #6: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.240621 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #7: protein, 30S ribosomal protein S4e

ProteinName: 30S ribosomal protein S4eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.820629 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #8: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.372613 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #9: protein, 30S ribosomal protein S6e

ProteinName: 30S ribosomal protein S6eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.760986 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #10: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.573713 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #11: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.602109 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #12: protein, 30S ribosomal protein S8e

ProteinName: 30S ribosomal protein S8eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.548031 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #13: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.358943 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #14: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.716666 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #15: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.111241 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #16: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.488537 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #17: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.025875 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #18: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.583785 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #19: protein, 30S ribosomal protein S14 type Z

ProteinName: 30S ribosomal protein S14 type ZRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.634088 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #20: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.219385 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #21: protein, 30S ribosomal protein S17e

ProteinName: 30S ribosomal protein S17eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.036431 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #22: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.453374 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #23: protein, 30S ribosomal protein S19e

ProteinName: 30S ribosomal protein S19eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.303977 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #24: protein, 30S ribosomal protein S24e

ProteinName: 30S ribosomal protein S24eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.458116 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #25: protein, 30S ribosomal protein S27e

ProteinName: 30S ribosomal protein S27eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.085514 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #26: protein, 30S ribosomal protein S28e

ProteinName: 30S ribosomal protein S28eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.971244 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #27: protein, Predicted zinc-ribbon RNA-binding protein involved in tr...

ProteinName: Predicted zinc-ribbon RNA-binding protein involved in translation
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.001247 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

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Component #28: nucleic-acid, 23S rRNA

nucleic acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AACGUCCCGC CCGGUGGCAA CUAAGC(4AC)GCC UGG(OMU)GGAUGG CUCGGCUCGG GGCGC(4AC)GACG AA(OMG)(OMG)GCGUGG CAAGCUGCGA UAAGCCCCGG CGAGGCGCAG GCAGCCGUCG AACCGGGGAU GCC(4AC)GAAUGG GACCUCCCGC GGCUUUUGCC ...Sequence:
AACGUCCCGC CCGGUGGCAA CUAAGC(4AC)GCC UGG(OMU)GGAUGG CUCGGCUCGG GGCGC(4AC)GACG AA(OMG)(OMG)GCGUGG CAAGCUGCGA UAAGCCCCGG CGAGGCGCAG GCAGCCGUCG AACCGGGGAU GCC(4AC)GAAUGG GACCUCCCGC GGCUUUUGCC GCACUCCCAG UCGGGAGGGG GAACGCGGGG AAUUGAAACA UCUUAGUACC (4AC)GCAGGAAAA G(A2M)AA(OMG)CAAAA GCGAUGCCGU UAGUAGGGGC GAC(4AC)GAAAG(OMC) GGCACAGGGC AAACUGAACC CCGGGCCGAA AGGUUCGGG(OMG) GAUGUGG(5MU)GU UGUAGGGCCC GCGGAGGAGC CCUGGGGGCG AAGC(4AC)GAAGU CCGCUGGAAC GC(OMG)GCG(B8T)CGG AGAG(OMG)GUGAA AGCCC(4AC)GUAG GCGUAAGCCC CCGAGCUCCU GCGGUGUCCC UGAGUAC(4AC)(OMG)U CGGUCGGAUA UC(4AC)GGCGGGA AGCUGGGAGG CA(OMU)CGGCUCC CAACCCUAAA UACGUCCCGA GACCGAU(A2M)GC GAACUAGUAC (4AC)GUG(A2M)GGGAA AGCUGAAAAG CACCC(LHH)GGGA GGGGGG(5MU)GAA AAGAGCCUGA A(OMG)CCAGGCGG (OMC)GAUAGGAGG G(5MU)GC(OMG)GCCCG AAAGGGUUGA CCCUCCCCGA AGGAAACACG GGCGAC(LHH)G(OMU)G GAGUACGAGG GGAGGUGACC GGGGUUGCAC CGUCCG(OMU)CUU GGAUCACGGG GCA(OMG)GGAGUU CACCCGAGCG GCGAGGUUAA GGGGGUCAAC CC(4AC)GAAG(OMC)CG CA(OMG)GGAAAC(4AC) GACAGGUCCG CAGCCCGUAA GGG(OMC)G(A2M)GGGA CG(OMG)GGUG(OMU)GA AAGCGCC(4AC)GG AGUCGCUCGG GUGAGACC(4AC)(OMG) AAGC(4AC)GGUCG AUCUAGCCCG GGGC(A2M)GGGUG AA(OMG)UCCCUCA ACAGAGGG(A2M)U GGAGGCC(4AC)GC UAGGGGUG(OMC)U G(A2M)CG(5MU)GCA(A2M)U UCGCUCCCGU GACCCCGGGC UAGGGGUGAA A(OMG)GCCAAUCG AGGC(4AC)GGCGA U(A2M)GCUGGUUC CCG(5MC)CGAAUU AUCCCCCAGG AUAGCCCGGC CGGAGGUAGG CAGUGGGGUA GAGCACUGAU UGGGGGUUUA GGGGGCGAAA GCCUCCGGCU CCCUGUCAAA CUCCGAACCC ACUGCCGCCG UAGAUGGCCG GAGUAGGGGG GCGG(5MU)GUAAG CCGUCACCCG AGAGG(OMG)GAAC AACCCAGACC GGGGUUAAGG CCCCAAAGUG CCGGCUAAGU GUUACUCCAA AGGGUGUCCC UGGCCUUAGA CAGCGGGGAG GUAGGCUUAG AAGCAGCCAU CCUUUAAAGA GUGCGUAACA GCUCACCCGU CGAGGUCAGG GGCCCCGAAA AUGG(A2M)CGGGG CUUAAGCCGG CCGCCGAGAC CCCGGCGCAC GGAC(4AC)GAUUG GUCCGUGA(OMU)C GGGUAGGCGG GCGUGC(4AC)GA(OMU) GGGGCGGAAG CCGGGC(4AC)GUG AGGUCCGGUG GACC(4AC)GUCGG UAUUGCGGAU CCUGC(4AC)G(OMG)G(A2M) GUAGCAGCAU AGCCGGGUGA GAAUCC(4AC)GGC (4AC)GC(4AC)GUAGGG GCCAGGGUUC CACGGCAAUG UUCGUCAGC(4AC) GUGGGUUAG(OMU) CGGUCCUAAC CCGACCCGUA ACUCGGCGUC GGGGAA(A2M)GGG AAAC(OMG)GGUUU AUAUUCCCGU AC(4AC)GCGG(5MU)GG (OMU)AGGUGC(OMG)GC AACGCAAGCC CGAGGGGUGA CGCCUCGGGG UAGGCGGACC GGUCCACAAG GCCGGCUAAG CGUAUAAGCC CGGGGAGUGC (4AC)GUAAUGGCG AGAACCGGGU GAAAGCGCGA AUGGCCUCCC GUAAGGGGGG UUCCG(5MC)CGAU CCCUGGGGCC CGUGAAAAGC CCCUCGGGAA CGAUCCACCG CGACCGUAC(OMC) GAGAACCGAC ACUGGUGCCC CUGGG(OMU)GAGA AGCCUAAGG(OMC) GUGUCGGG(OMG)G AAACCCAGC(4AC) GAGGGAACU(OMC) GGCAAAUUGG CCCCGUAACU UCGGGAGAAG GGGUGCCUGC GGGUGUGUAA CCCGCAGGUC GCAGUGACUA G(OMG)GGGGCC(4AC)G ACUG(5MU)UUAGU AAAAACACAG GUCCCAGCUA GCC(4AC)GAAAG(OMG) GUUUGUACUG GG(OMG)C(4AC)GACGC CUGC(5MC)CAG(OMU)G CCGGUAUGUG AAGCCCGGGU ACAACCGGGU GAAGCACCG(OMG) UAAAC(OMG)G(OMC)(OMG)G GGGUAACUAU AACC(5MC)UCUUA AGGUAG(OMC)GAA AUUC(5MC)UUGUC GGUUAAAUG(5MC) CGAC(5MC)UGCAU GAAUGGCGUA ACGAGGUCCC CACUGUCCCC GGCUGGGGCC (4AC)GG(OMC)GAAACC UCUGCCAGGC GCAUAUGCCU G(OMG)GACCUC(4AC)G GUGGGAA(OMG)CG AAGACCCCAU GGAGCUUUAC UGCAGCCUGC CGUUGCCGUA CGGCGGGGGG UGCGCAGCGU AGGCGGGAGG CGUCGAAGCC CGCCCUCCGG GGCGGGUGGA GCCGCCCAUG AGACACCGCC CACCCUCUGC CGUACGGCUA ACCCGCGGAA GCG(OMG)GGACAG CGGUAGGUGG GCAGUUUGGC UG(OMG)GGCGGCA CACCCUCGAA AAGGUAUC(OMG)A GGG(5MU)GCCC(OMU)A AGGUCGGCUC AGGCGGGUCA GGAAUCCGCC GUAGAGUGCA AGGGCAAAAG CCGGCCUGAC UGGACC(LHH)GUA ACAGAGGCGG GUCCAGCCGC GAAAGCGUGG CCUAGCGAAC CCCUGUGCCU CCCCGGUGGG (OMG)GCCAG(OMG)(OMG)AU GACAGAAAAG C(OMU)AC(OMC)CUGG(OMG) GA(4SU)AACAGAG UCGUCUC(OMG)GG (OMC)GAGAGCCCA (4SU)AUCGACCC(4AC) GAGG(OMC)UUGCU ACCU(5MC)GCUG(OMU) CGGCUCUUCC CAUCCUGGC(OMC) CUGCAGCAGG GGCCAAGGGU GGGGG(OMU)(OMG)UUC ACCCAUUAAA G(OMG)GGAACGUG AGCUGGG(5MU)UU AGACCGUCGU G(A2M)GACAGGUC GGAUGCUAUC UACCGGA(OMG)GU GUUGGCCGCC UGAG(OMG)GGAAG GCUCCCCCAG UACGAGAGGA ACAGGGAGC(4AC) GCGGCCUCUG GUCUAC(4AC)GGU UGUCCUACAG GGCAUAGCCG GGCAGCUACG C(4AC)GCAGC(4AC)GA UAAGGCCUGA AAGCAUCUAA GG(5MC)CGAAGCG GCCCCCGAAA ACAGGCGGCC ACUCCUGGGC GUUGGGCCUG GGCGACCGGU CCGUUGCCCA GGACGAGGGC CCGGGAAGAA GACC(LHH)GGUUG AUGGGGCGGG GAUGUAAGCG GGAAGGGAAA C(4AC)GACC(4AC)GUU CAGUCUGC(4AC)G CUCCCAACAG CC(4AC)GAGUGCU ACCGGGC
MassTheoretical: 990.337312 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #29: nucleic-acid, 5S rRNA

nucleic acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUACGGCGG CCAUAGCGGC GGGGCCACAC CCGGUCUCGU UUCGACCCCG GAAGUUAAGC CCGCCAGCGU UCCCGGGUGU ACUGCCCUCC GAGAGGGGGC GGGAAACCGG GAACGCCGCC GGCCAC
MassTheoretical: 40.744309 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #30: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.092432 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #31: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.118637 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #32: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.768604 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #33: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.02757 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #34: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.888271 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #35: protein, 50S ribosomal protein L7Ae

ProteinName: 50S ribosomal protein L7AeRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.454623 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #36: protein, 50S ribosomal protein L10e

ProteinName: 50S ribosomal protein L10eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.116596 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #37: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.316173 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #38: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.181888 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #39: protein, 50S ribosomal protein L14e

ProteinName: 50S ribosomal protein L14eRibosome / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.968527 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #40: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.571436 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #41: protein, 50S ribosomal protein L15e

ProteinName: 50S ribosomal protein L15eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.607863 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #42: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.895449 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #43: protein, 50S ribosomal protein L18e

ProteinName: 50S ribosomal protein L18eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.799152 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #44: protein, 50S ribosomal protein L19e

ProteinName: 50S ribosomal protein L19eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.667176 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #45: protein, 50S ribosomal protein L18Ae

ProteinName: 50S ribosomal protein L18AeRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.227708 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #46: protein, 50S ribosomal protein L21e

ProteinName: 50S ribosomal protein L21eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.290313 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #47: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.838777 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #48: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.915769 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #49: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.225809 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #50: protein, 50S ribosomal protein L24e

ProteinName: 50S ribosomal protein L24eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.111553 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #51: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.937539 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #52: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.856193 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #53: protein, 50S ribosomal protein L30e

ProteinName: 50S ribosomal protein L30eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.97282 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #54: protein, 50S ribosomal protein L31e

ProteinName: 50S ribosomal protein L31eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.354293 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #55: protein, 50S ribosomal protein L32e

ProteinName: 50S ribosomal protein L32eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.65448 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #56: protein, 50S ribosomal protein L34e

ProteinName: 50S ribosomal protein L34eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.558783 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #57: protein, 50S ribosomal protein L37Ae

ProteinName: 50S ribosomal protein L37AeRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.24004 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #58: protein, 50S ribosomal protein L37e

ProteinName: 50S ribosomal protein L37eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.470875 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #59: protein, 50S ribosomal protein L39e

ProteinName: 50S ribosomal protein L39eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.262679 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #60: protein, 50S ribosomal protein L40e

ProteinName: 50S ribosomal protein L40eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.781971 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #61: protein, LSU ribosomal protein L41E

ProteinName: LSU ribosomal protein L41E / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.051409 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #62: protein, 50S ribosomal protein L44e

ProteinName: 50S ribosomal protein L44eRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.204441 kDa
SourceSpecies: Thermococcus kodakarensis (archaea)

+
Component #63: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #64: ligand, water

LigandName: water / Number of Copies: 2367 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.25 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
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: 34 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (calibrated) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 53737
3D reconstructionSoftware: RELION / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

+
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