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- EMDB-4474: Cryo-EM structure of the mRNA translating and degrading yeast 80S... -

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Basic information

Entry
Database: EMDB / ID: 4474
TitleCryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex
Map data
SampleYeast 80S ribosome in complex with the Xrn11 exoribonuclease obtained from natural source.
  • ribosome
  • mRNAMessenger RNA
  • (5'-3' exoribonuclease ...) x 2
  • P-site tRNA
  • E-site tRNA
  • (nucleic-acidNucleic acid) x 7
  • (60S ribosomal protein ...) x 40
  • Ubiquitin-60S ribosomal protein L40
  • (40S ribosomal protein ...) x 30
  • Rps5p
  • Ubiquitin-40S ribosomal protein S31
  • Guanine nucleotide-binding protein subunit beta-like protein
  • (ligand) x 2
Function / homologyWinged helix DNA-binding domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein L36e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L21 superfamily ...Winged helix DNA-binding domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein L38e superfamily / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S19e domain superfamily / Ribosomal protein L36e domain superfamily / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L14 superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L18e signature. / Winged helix-like DNA-binding domain superfamily / Ribosomal protein L32e superfamily / WD40-repeat-containing domain superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein S26e superfamily / Ribosomal protein L19, eukaryotic / Ribosomal protein S7p/S5e / Ribosomal protein S15 / Ribosomal protein L3 / Ribosomal protein L5 / Ribosomal protein L23 / Ribosomal protein S14p/S29e / Ribosomal protein L16p/L10e / Ubiquitin family / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e / Ribosomal protein S19 / Ribosomal protein S3, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S12/S23 / Ribosomal protein L34Ae superfamily / Exoribonuclease 1, domain 3 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein L7/L30 / Ribosomal protein L14 / 60S ribosomal protein L19 / Ribosomal protein L30/YlxQ / Ribosomal protein L35A superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L40e superfamily / S27a-like superfamily / Ribosomal protein S21e superfamily / Ribosomal protein L7, eukaryotic/archaeal / 40S ribosomal protein S11, N-terminal / Ribosomal protein L30p/L7e / Ribosomal protein S5 domain 2-type fold / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein S8e/ribosomal biogenesis NSA2 / 60S ribosomal protein L18a/ L20, eukaryotes / Ribosomal protein L18e, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein S19 conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L5 domain superfamily / Ribosomal protein L39e, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein S17, conserved site / Ribosomal protein L14P, conserved site / Ubiquitin / Ubiquitin conserved site / Ribosomal protein L3, conserved site / WD40 repeat, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L30e, conserved site / 40S ribosomal protein S4, C-terminal domain / 5'-3' exoribonuclease / Ribosomal protein L5, N-terminal / Ribosomal protein L5, C-terminal / Ribosomal protein L15 / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsTesina P / Heckel E / Cheng J / Buschauer R / Kater L / Berninghausen O / Becker T / Beckmann R
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structure of the 80S ribosome-Xrn1 nuclease complex
Authors: Tesina P / Heckel E / Cheng J / Buschauer R / Kater L / Berninghausen O / Fromont-Racine M / Beatrix B / Jacquier A / Becker T / Beckmann R
Validation ReportPDB-ID: 6q8y

SummaryFull reportAbout validation report
DateDeposition: Dec 16, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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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-6q8y
  • 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

Fileemd_4474.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.08 Å/pix.
= 433.6 Å
400 pix
1.08 Å/pix.
= 433.6 Å
400 pix
1.08 Å/pix.
= 433.6 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 Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.23195499 - 0.4696315
Average (Standard dev.)0.0010171264 (0.019143192)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 433.6 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z433.600433.600433.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2320.4700.001

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Supplemental data

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Sample components

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Entire Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obta...

EntireName: Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obtained from natural source.
Number of components: 90

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Component #1: protein, Yeast 80S ribosome in complex with the Xrn11 exoribonucl...

ProteinName: Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obtained from natural source.
Recombinant expression: No

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Component #2: protein, ribosome

ProteinName: ribosome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, 5'-3' exoribonuclease Xrn1

ProteinName: 5'-3' exoribonuclease Xrn1 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, P-site tRNA

ProteinName: P-site tRNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, E-site tRNA

ProteinName: E-site tRNA / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #7: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUCUGGUUG AUCCUGCCAG UAGUCAUAUG CUUGUCUCAA AGAUUAAGCC AUGCAUGUCU AAGUAUAAGC AAUUUAUACA GUGAAACUGC GAAUGGCUCA UUAAAUCAGU UAUCGUUUAU UUGAUAGUUC CUUUACUACA UGGUAUAACU GUGGUAAUUC UAGAGCUAAU ACAUGCUUAA AAUCUCGACC CUUUGGAAGA GAUGUAUUUA UUAGAUAAAA AAUCAAUGUC UUCGGACUCU UUGAUGAUUC AUAAUAACUU UUCGAAUCGC AUGGCCUUGU GCUGGCGAUG GUUCAUUCAA AUUUCUGCCC UAUCAACUUU CGAUGGUAGG AUAGUGGCCU ACCAUGGUUU CAACGGGUAA CGGGGAAUAA GGGUUCGAUU CCGGAGAGGG AGCCUGAGAA ACGGCUACCA CAUCCAAGGA AGGCAGCAGG CGCGCAAAUU ACCCAAUCCU AAUUCAGGGA GGUAGUGACA AUAAAUAACG AUACAGGGCC CAUUCGGGUC UUGUAAUUGG AAUGAGUACA AUGUAAAUAC CUUAACGAGG AACAAUUGGA GGGCAAGUCU GGUGCCAGCA GCCGCGGUAA UUCCAGCUCC AAUAGCGUAU AUUAAAGUUG UUGCAGUUAA AAAGCUCGUA GUUGAACUUU GGGCCCGGUU GGCCGGUCCG AUUUUUCGUG UACUGGAUUU CCAACGGGGC CUUUCCUUCU GGCUAACCUU GAGUCCUUGU GGCUCUUGGC GAACCAGGAC UUUUACUUUG AAAAAAUUAG AGUGUUCAAA GCAGGCGUAU UGCUCGAAUA UAUUAGCAUG GAAUAAUAGA AUAGGACGUU UGGUUCUAUU UUGUUGGUUU CUAGGACCAU CGUAAUGAUU AAUAGGGACG GUCGGGGGCA UCAGUAUUCA AUUGUCAGAG GUGAAAUUCU UGGAUUUAUU GAAGACUAAC UACUGCGAAA GCAUUUGCCA AGGACGUUUU CAUUAAUCAA GAACGAAAGU UAGGGGAUCG AAGAUGAUCA GAUACCGUCG UAGUCUUAAC CAUAAACUAU GCCGACUAGG GAUCGGGUGG UGUUUUUUUA AUGACCCACU CGGCACCUUA CGAGAAAUCA AAGUCUUUGG GUUCUGGGGG GAGUAUGGUC GCAAGGCUGA AACUUAAAGG AAUUGACGGA AGGGCACCAC CAGGAGUGGA GCCUGCGGCU UAAUUUGACU CAACACGGGG AAACUCACCA GGUCCAGACA CAAUAAGGAU UGACAGAUUG AGAGCUCUUU CUUGAUUUUG UGGGUGGUGG UGCAUGGCCG UUCUUAGUUG GUGGAGUGAU UUGUCUGCUU AAUUGCGAUA ACGAACGAGA CCUUAACCUA CUAAAUAGUG GUGCUAGCAU UUGCUGGUUA UCCACUUCUU AGAGGGACUA UCGGUUUCAA GCCGAUGGAA GUUUGAGGCA AUAACAGGUC UGUGAUGCCC UUAGACGUUC UGGGCCGCAC GCGCGCUACA CUGACGGAGC CAGCGAGUCU AACCUUGGCC GAGAGGUCUU GGUAAUCUUG UGAAACUCCG UCGUGCUGGG GAUAGAGCAU UGUAAUUAUU GCUCUUCAGC GAGGAAUUCC UAGUAAGCGC AAGUCAUCAG CUUGCGUUGA UUACGUCCCU GCCCUUUGUA CACACCGCCC GUCGCUAGUA CCGAUUGAAU GGCUUAGUGA GGCCUCAGGA UCUGCUUAGA GAAGGGGGCA ACUCCAUCUC AGAGCGGAGA AUUUGGACAA ACUUGGUCAU UUAGAGGAAC UAAAAGUCGU AACAAGGUUU CCGUAGGUGA ACCUGCGGAA GGAUCAU
MassTheoretical: 578.836375 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.814998 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.362755 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, 60S ribosomal protein L36-A

ProteinName: 60S ribosomal protein L36-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.151259 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, 60S ribosomal protein L9-A

ProteinName: 60S ribosomal protein L9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.605061 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.84317 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.746199 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, 60S ribosomal protein L11-B

ProteinName: 60S ribosomal protein L11-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.266082 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.771176 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.714363 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.885234 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.134588 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.227444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.976794 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.437166 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.032321 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #23: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.115462 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #24: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.351162 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #25: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.630471 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #26: protein, 60S ribosomal protein L41-B

ProteinName: 60S ribosomal protein L41-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.354243 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #27: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.981756 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #28: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.028951 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #29: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.560688 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #30: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.217289 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #31: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.458322 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #32: protein, 40S ribosomal protein S21-A

ProteinName: 40S ribosomal protein S21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.758829 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #33: protein, 40S ribosomal protein S22-A

ProteinName: 40S ribosomal protein S22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.518867 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #34: protein, 40S ribosomal protein S23-A

ProteinName: 40S ribosomal protein S23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.942699 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #35: protein, 40S ribosomal protein S24-A

ProteinName: 40S ribosomal protein S24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.045483 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #36: protein, 40S ribosomal protein S26-B

ProteinName: 40S ribosomal protein S26-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.022989 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #37: protein, 40S ribosomal protein S27-A

ProteinName: 40S ribosomal protein S27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.762195 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #38: protein, 40S ribosomal protein S30-A

ProteinName: 40S ribosomal protein S30-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.779086 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #39: protein, 5'-3' exoribonuclease 1

ProteinName: 5'-3' exoribonuclease 1XRN1 (gene) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 107.653734 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #40: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAUCCUGGAU GGAACGA
MassTheoretical: 5.49035 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #41: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUCCUCGUGG CCCAAUGGUC ACGGCGUCUG GCUACGAACC AGAAGAUUCC AGGUUCAAGU CCUGGCGGGG AAGCCA
MassTheoretical: 24.468551 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #42: nucleic-acid, E-site tRNA

Nucleic-acidName: E-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCCGAUAUAG CGUAACGGCU AUCACAUCAC GCUUUCACCG UGGAGACCGG GGUUCGACUC CCCGUAUCGG AGCCA
MassTheoretical: 24.004262 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #43: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.558344 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #44: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.719602 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #45: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478059 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #46: protein, 60S ribosomal protein L31-A

ProteinName: 60S ribosomal protein L31-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.649754 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #47: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.279271 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #48: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.027926 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #49: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.631121 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #50: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.478054 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #51: protein, 60S ribosomal protein L20-A

ProteinName: 60S ribosomal protein L20-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.478852 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #52: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.633633 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #53: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.148066 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #54: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.045935 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #55: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.263863 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #56: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.869369 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #57: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.608831 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #58: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.240377 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #59: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.811444 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #60: nucleic-acid, 25S ribosomal RNA

Nucleic-acidName: 25S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUGACCUC AAAUCAGGUA GGAGUACCCG CUGAACUUAA GCAUAUCAAU AAGCGGAGGA AAAGAAACCA ACCGGGAUUG CCUUAGUAAC GGCGAGUGAA GCGGCAAAAG CUCAAAUUUG AAAUCUGGUA CCUUCGGUGC CCGAGUUGUA AUUUGGAGAG GGCAACUUUG GGGCCGUUCC UUGUCUAUGU UCCUUGGAAC AGGACGUCAU AGAGGGUGAG AAUCCCGUGU GGCGAGGAGU GCGGUUCUUU GUAAAGUGCC UUCGAAGAGU CGAGUUGUUU GGGAAUGCAG CUCUAAGUGG GUGGUAAAUU CCAUCUAAAG CUAAAUAUUG GCGAGAGACC GAUAGCGAAC AAGUACAGUG AUGGAAAGAU GAAAAGAACU UUGAAAAGAG AGUGAAAAAG UACGUGAAAU UGUUGAAAGG GAAGGGCAUU UGAUCAGACA UGGUGUUUUG UGCCCUCUGC UCCUUGUGGG UAGGGGAAUC UCGCAUUUCA CUGGGCCAGC AUCAGUUUUG GUGGCAGGAU AAAUCCAUAG GAAUGUAGCU UGCCUCGGUA AGUAUUAUAG CCUGUGGGAA UACUGCCAGC UGGGACUGAG GACUGCGACG UAAGUCAAGG AUGCUGGCAU AAUGGUUAUA UGCCGCCCGU CUUGAAACAC GGACCAAGGA GUCUAACGUC UAUGCGAGUG UUUGGGUGUA AAACCCAUAC GCGUAAUGAA AGUGAACGUA GGUUGGGGCC UCGCAAGAGG UGCACAAUCG ACCGAUCCUG AUGUCUUCGG AUGGAUUUGA GUAAGAGCAU AGCUGUUGGG ACCCGAAAGA UGGUGAACUA UGCCUGAAUA GGGUGAAGCC AGAGGAAACU CUGGUGGAGG CUCGUAGCGG UUCUGACGUG CAAAUCGAUC GUCGAAUUUG GGUAUAGGGG CGAAAGACUA AUCGAACCAU CUAGUAGCUG GUUCCUGCCG AAGUUUCCCU CAGGAUAGCA GAAGCUCGUA UCAGUUUUAU GAGGUAAAGC GAAUGAUUAG AGGUUCCGGG GUCGAAAUGA CCUUGACCUA UUCUCAAACU UUAAAUAUGU AAGAAGUCCU UGUUACUUAA UUGAACGUGG ACAUUUGAAU GAAGAGCUUU UAGUGGGCCA UUUUUGGUAA GCAGAACUGG CGAUGCGGGA UGAACCGAAC GUAGAGUUAA GGUGCCGGAA UACACGCUCA UCAGACACCA CAAAAGGUGU UAGUUCAUCU AGACAGCCGG ACGGUGGCCA UGGAAGUCGG AAUCCGCUAA GGAGUGUGUA ACAACUCACC GGCCGAAUGA ACUAGCCCUG AAAAUGGAUG GCGCUCAAGC GUGUUACCUA UACUCUACCG UCAGGGUUGA UAUGAUGCCC UGACGAGUAG GCAGGCGUGG AGGUCAGUGA CGAAGCCUAG ACCGUAAGGU CGGGUCGAAC GGCCUCUAGU GCAGAUCUUG GUGGUAGUAG CAAAUAUUCA AAUGAGAACU UUGAAGACUG AAGUGGGGAA AGGUUCCACG UCAACAGCAG UUGGACGUGG GUUAGUCGAU CCUAAGAGAU GGGGAAGCUC CGUUUCAAAG GCCUGAUUUU AUGCAGGCCA CCAUCGAAAG GGAAUCCGGU UAAGAUUCCG GAACCUGGAU AUGGAUUCUU CACGGUAACG UAACUGAAUG UGGAGACGUC GGCGCGAGCC CUGGGAGGAG UUAUCUUUUC UUCUUAACAG CUUAUCACCC CGGAAUUGGU UUAUCCGGAG AUGGGGUCUU AUGGCUGGAA GAGGCCAGCA CCUUUGCUGG CUCCGGUGCG CUUGUGACGG CCCGUGAAAA UCCACAGGAA GGAAUAGUUU UCAUGCCAGG UCGUACUGAU AACCGCAGCA GGUCUCCAAG GUGAACAGCC UCUAGUUGAU AGAAUAAUGU AGAUAAGGGA AGUCGGCAAA AUAGAUCCGU AACUUCGGGA UAAGGAUUGG CUCUAAGGGU CGGGUAGUGA GGGCCUUGGU CAGACGCAGC GGGCGUGCUU GUGGACUGCU UGGUGGGGCU UGCUCUGCUA GGCGGACUAC UUGCGUGCCU UGUUGUAGAC GGCCUUGGUA GGUCUCUUGU AGACCGUCGC UUGCUACAAU UAACGAUCAA CUUAGAACUG GUACGGACAA GGGGAAUCUG ACUGUCUAAU UAAAACAUAG CAUUGCGAUG GUCAGAAAGU GAUGUUGACG CAAUGUGAUU UCUGCCCAGU GCUCUGAAUG UCAAAGUGAA GAAAUUCAAC CAAGCGCGGG UAAACGGCGG GAGUAACUAU GACUCUCUUA AGGUAGCCAA AUGCCUCGUC AUCUAAUUAG UGACGCGCAU GAAUGGAUUA ACGAGAUUCC CACUGUCCCU AUCUACUAUC UAGCGAAACC ACAGCCAAGG GAACGGGCUU GGCAGAAUCA GCGGGGAAAG AAGACCCUGU UGAGCUUGAC UCUAGUUUGA CAUUGUGAAG AGACAUAGAG GGUGUAGAAU AAGUGGGAGC UUCGGCGCCA GUGAAAUACC ACUACCUUUA UAGUUUCUUU ACUUAUUCAA UGAAGCGGAG CUGGAAUUCA UUUUCCACGU UCUAGCAUUC AAGGUCCCAU UCGGGGCUGA UCCGGGUUGA AGACAUUGUC AGGUGGGGAG UUUGGCUGGG GCGGCACAUC UGUUAAACGA UAACGCAGAU GUCCUAAGGG GGGCUCAUGG AGAACAGAAA UCUCCAGUAG AACAAAAGGG UAAAAGCCCC CUUGAUUUUG AUUUUCAGUG UGAAUACAAA CCAUGAAAGU GUGGCCUAUC GAUCCUUUAG UCCCUCGGAA UUUGAGGCUA GAGGUGCCAG AAAAGUUACC ACAGGGAUAA CUGGCUUGUG GCAGUCAAGC GUUCAUAGCG ACAUUGCUUU UUGAUUCUUC GAUGUCGGCU CUUCCUAUCA UACCGAAGCA GAAUUCGGUA AGCGUUGGAU UGUUCACCCA CUAAUAGGGA ACGUGAGCUG GGUUUAGACC GUCGUGAGAC AGGUUAGUUU UACCCUACUG AUGAAUGUUA CCGCAAUAGU AAUUGAACUU AGUACGAGAG GAACAGUUCA UUCGGAUAAU UGGUUUUUGC GGCUGUCUGA UCAGGCAUUG CCGCGAAGCU ACCAUCCGCU GGAUUAUGGC UGAACGCCUC UAAGUCAGAA UCCAUGCUAG AACGCGGUGA UUUCUUUGCU CCACACAAUA UAGAUGGAUA CGAAUAAGGC GUCCUUGUGG CGUCGCUGAA CCAUAGCAGG CUAGCAACGG UGCACUUGGC GGAAAGGCCU UGGGUGCUUG CUGGCGAAUU GCAAUGUCAU UUUGCGUGGG GAUAAAUCAU UUGUAUACGA CUUAGAUGUA CAACGGGGUA UUGUAAGCAG UAGAGUAGCC UUGUUGUUAC GAUCUGCUGA GAUUAAGCCU UUGUUGUCUG AUUUGU
MassTheoretical: 1.097493875 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #61: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGUUGCGGCC AUAUCUACCA GAAAGCACCG UUUCCCGUCC GAUCAACUGU AGUUAAGCUG GUAAGAGCCU GACCGAGUAG UGUAGUGGGU GACCAUACGC GAAACUCAGG UGCUGCAAUC U
MassTheoretical: 38.951105 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #62: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AAACUUUCAA CAACGGAUCU CUUGGUUCUC GCAUCGAUGA AGAACGCAGC GAAAUGCGAU ACGUAAUGUG AAUUGCAGAA UUCCGUGAAU CAUCGAAUCU UUGAACGCAC AUUGCGCCCC UUGGUAUUCC AGGGGGCAUG CCUGUUUGAG CGUCAUUU
MassTheoretical: 50.682922 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #63: protein, 40S ribosomal protein S3

ProteinName: 40S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.702791 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #64: protein, Rps5p

ProteinName: Rps5p / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.908338 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #65: protein, 40S ribosomal protein S10-A

ProteinName: 40S ribosomal protein S10-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.5711 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #66: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.028008 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #67: protein, 40S ribosomal protein S15

ProteinName: 40S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870396 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #68: protein, 40S ribosomal protein S16-A

ProteinName: 40S ribosomal protein S16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.659216 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #69: protein, 40S ribosomal protein S17-A

ProteinName: 40S ribosomal protein S17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.268545 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #70: protein, 40S ribosomal protein S18-A

ProteinName: 40S ribosomal protein S18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.239629 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #71: protein, 40S ribosomal protein S20

ProteinName: 40S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.190175 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #72: protein, 40S ribosomal protein S25-A

ProteinName: 40S ribosomal protein S25-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.001377 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #73: protein, 40S ribosomal protein S28-A

ProteinName: 40S ribosomal protein S28-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.116281 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #74: protein, 40S ribosomal protein S29-A

ProteinName: 40S ribosomal protein S29-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.335303 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #75: protein, Ubiquitin-40S ribosomal protein S31

ProteinName: Ubiquitin-40S ribosomal protein S31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.70461 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #76: protein, Guanine nucleotide-binding protein subunit beta-like protein

ProteinName: Guanine nucleotide-binding protein subunit beta-like protein
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.710023 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #77: protein, 40S ribosomal protein S0-A

ProteinName: 40S ribosomal protein S0-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.255527 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #78: protein, 40S ribosomal protein S1-A

ProteinName: 40S ribosomal protein S1-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.312199 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #79: protein, 40S ribosomal protein S2

ProteinName: 40S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.718654 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #80: protein, 40S ribosomal protein S4-A

ProteinName: 40S ribosomal protein S4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.338133 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #81: protein, 40S ribosomal protein S6-A

ProteinName: 40S ribosomal protein S6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.895072 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #82: protein, 40S ribosomal protein S7-A

ProteinName: 40S ribosomal protein S7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.000492 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #83: protein, 40S ribosomal protein S8-A

ProteinName: 40S ribosomal protein S8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.406609 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #84: protein, 40S ribosomal protein S9-A

ProteinName: 40S ribosomal protein S9-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.366689 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #85: protein, 40S ribosomal protein S11-A

ProteinName: 40S ribosomal protein S11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.654738 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #86: protein, 40S ribosomal protein S13

ProteinName: 40S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.928748 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #87: protein, 40S ribosomal protein S14-B

ProteinName: 40S ribosomal protein S14-BRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.446426 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #88: protein, 40S ribosomal protein S19-A

ProteinName: 40S ribosomal protein S19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.81093 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #89: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #90: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 217000
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
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