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- EMDB-0098: tRNA translocation by the eukaryotic 80S ribosome and the impact ... -

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Basic information

Entry
Database: EMDB / ID: 0098
TitletRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1)
Map data
Sampletranslocation intermediate TI-POST-1:
Ribosome / mRNAMessenger RNA / tRNATransfer RNA / (nucleic-acidNucleic acid) x 7 / (Ribosomal protein ...) x 72 / (40S ribosomal protein ...) x 4 / 60S ribosomal protein L27 / Ribosomal protein / eukaryotic elongation factor 2 (eEF2) / (ligand) x 3
Function / homologyRibosomal protein L1, conserved site / Ribosomal protein S8 superfamily / Ribosomal protein L15e core domain superfamily / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily ...Ribosomal protein L1, conserved site / Ribosomal protein S8 superfamily / Ribosomal protein L15e core domain superfamily / 30s ribosomal protein S13, C-terminal / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein S28e conserved site / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / 40S ribosomal protein S11, N-terminal / WD40-repeat-containing domain superfamily / Ribosomal protein L1-like / Ribosomal protein L32e superfamily / Winged helix-like DNA-binding domain superfamily / Ribosomal protein S17e-like superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ribosomal protein S7 domain / Ribosomal protein L2, archaeal-type / Ribosomal protein L24e/L24 superfamily / Ribosomal protein S7, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein L31e, conserved site / Ribosomal protein L39e, conserved site / G-protein beta WD-40 repeat / Ribosomal protein L11, C-terminal / Ribosomal protein L39e domain superfamily / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein S4/S9 / Ribosomal protein L5 domain superfamily / Ribosomal protein S15P / Ribosomal protein L24e, conserved site / Ribosomal protein L31e domain superfamily / S27a-like superfamily / Ribosomal protein L27e superfamily / Ribosomal protein S13, conserved site / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S7e / S4 domain / Ribosomal protein S27a / Ribosomal protein L32 / Ribosomal L27e protein family / Ribosomal L37ae protein family / Ribosomal protein L37e / S25 ribosomal protein / Plectin/S10 domain / Ribosomal protein L11, N-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal_S17 N-terminal / Ribosomal protein L24e / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L14 signature. / Ribosomal protein L39e signature. / Ribosomal protein S7 signature. / Ribosomal protein S8 signature. / Ribosomal protein S12 signature. / Ribosomal protein S17 signature. / Ubiquitin domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L11 signature. / Ribosomal protein S15 signature. / Ribosomal protein L2 signature. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S28e / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S17 / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S12/S23 / Ribosomal protein S7p/S5e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein S14p/S29e / Ribosomal protein L5 / Ribosomal protein L11, RNA binding domain / Ribosomal protein S15 / WD domain, G-beta repeat
Function and homology information
SourceOryctolagus cuniculus (rabbit) / Enterobacteria phage SP6 (bacteriophage) / Saccharomyces cerevisiae (baker's yeast) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsFlis J / Holm M / Rundlet EJ / Loerke J / Hilal T / Dabrowski M / Buerger J / Mielke T / Blanchard SC / Spahn CMT / Budkevich TV
CitationJournal: Cell Rep / Year: 2018
Title: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis.
Authors: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich
Abstract: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site.
Validation ReportPDB-ID: 6gz3

SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2018 / Header (metadata) release: Dec 5, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gz3
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0098.map.gz (map file in CCP4 format, 265721 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
405 pix
0.98 Å/pix.
= 394.875 Å
405 pix
0.98 Å/pix.
= 394.875 Å
405 pix
0.98 Å/pix.
= 394.875 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.975 Å
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-3.646757 - 11.638655999999999
Average (Standard dev.)0.34719723 (0.655024)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions405405405
Origin0.00.00.0
Limit404.0404.0404.0
Spacing405405405
CellA=B=C: 394.875 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9750.9750.975
M x/y/z405405405
origin x/y/z0.0000.0000.000
length x/y/z394.875394.875394.875
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS405405405
D min/max/mean-3.64711.6390.347

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Supplemental data

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Sample components

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Entire translocation intermediate TI-POST-1

EntireName: translocation intermediate TI-POST-1 / Number of components: 93

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Component #1: protein, translocation intermediate TI-POST-1

ProteinName: translocation intermediate TI-POST-1 / Recombinant expression: No
MassTheoretical: 4.3 MDa

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Component #2: protein, Ribosome

ProteinName: Ribosome / Recombinant expression: No
SourceSpecies: Oryctolagus cuniculus (rabbit)

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Component #3: protein, mRNA

ProteinName: mRNAMessenger RNA / Recombinant expression: No
SourceSpecies: Enterobacteria phage SP6 (bacteriophage)
Source (engineered)Expression System: Enterobacteria phage SP6 (bacteriophage)

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Component #4: protein, tRNA

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

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Component #5: nucleic-acid, 28S ribosomal RNA

Nucleic-acidName: 28S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGACCUCA GAUCAGACGU GGCGACCCGC UGAAUUUAAG CAUAUUAGUC AGCGGAGGAA AAGAAACUAA CCAGGAUUCC CUCAGUAACG GCGAGUGAAC AGGGAAGAGC CCAGCGCCGA AUCCCCGCCC CGCGGGGCGC GGGACAUGUG GCGUACGGAA GACCCGCUCC CCGGCGCCGC UCGUGGGGGG CCCAAGUCCU UCUGAUCGAG GCCCAGCCCG UGGACGGUGU GAGGCCGGUA GCGGCCCCCG GCGCGCGCCC GGGUCUUCCC GGAGUCGGGU UGCUUGGGAA UGCAGCCCAA AGCGGGUGGU AAACUCCAUC UAAGGCUAAA UACCGGCACG AGACCGAUAG UCAACAAGUA CCGUAAGGGA AAGUUGAAAA GAACUUUGAA GAGAGAGUUC AAGAGGGCGU GAAACCGUUA AGAGGUAAAC GGGUGGGGUC CGCGCAGUCC GCCCGGAGGA UUCAACCCGG CGGCGGGUCC GGCCGUGUCG GCGGCCCGGC GGAUCUUUCC CGCCCCCGGG GUCGGCGGGG GACCGUCCCC CGGACCGGCG ACCGGCCGCC GCCGGGCGCA UUUCCAGGCG GUGCGCCGCG ACCGGCUCCG GGACGGCUGG GAAGGCCCGG CGGGGAAGGU GGCUCGGGGC CCCCGAGUGU UACAGCCCCC CCGGCAGCAG CACUCGCCGA AUCCCGGGGC CGAGGGAGCG AGACCCGUCG CCGCGCUCUC CCCCCUGGGG GGGCCGGGCC ACCCCUCCCA CGGCGCGACC GCUCUCCCAG GGGGCGGGGC GGACUGUCCC CAGUGCGCCC CGGGCGGGUC GCGCCGUCGG GCCCGGGGGG CCACGCGCGC GUCCCGGGAC GGCGGAGCGA GCGCACGGGG UCGGCGGCGA CGUCGGCUAC CCACCCGACC CGUCUUGAAA CACGGACCAA GGAGUCUAAC ACGUGCGCGA GUCGGGGGCU CGCACGAAAG CCGCCGUGGC GCAAUGAAGG UGAAGGCCGG CGCGCUCGCC GGCCGAGGUG GGAUCCCGAG GCCUCUCCAG UCCGCCGAGG GGCACCACCG GCCCGUCUCG CCCGCCGCGC CGGGGAGGUG GAGCACGAGC GCACGUGUUA GGACCCGAAA GAUGGUGAAC UAUGCCUGGG CAGGGCGAAG CCAGAGGAAA CUCUGGUGGA GGUCCGUAGC GGUCCUGACG UGCAAAUCGG UCGUCCGACC UGGGUAUAGG GGCGAAAGAC UAAUCGAACC AUCUAGUAGC UGGUUCCCUC CGAAGUUUCC CUCAGGAUAG CUGGCGCUCU CGCCCACGCA GUUUUAUCCG GUAAAGCGAA UGAUUAGAGG UCUUGGGGCC GAAACGAUCU CAACCUAUUC UCAAACUUUA AAUGGGUAAG AAGCCCGGCU CGCUGGCGUG GAGCCGGGGU GGAAUGCGAG UGCCUAGUGG GCCACUUUUG GUAAGCAGAA CUGGCGCUGC GGGAUGAACC GAACGCCGGG UUAAGGCGCC CGAUGCCGAC GCUCAUCAGA CCCCAGAAAA GGUGUUGGUU GAUAUAGACA GCAGGACGGU GGCCAUGGAA GUCGGAAUCC GCUAAGGAGU GUGUAACAAC UCACCUGCCG AAUCAACUAG CCCUGAAAAU GGAUGGCGCU GGAGCGUCGG GCCCAUACCC GGCCGUCGCC GGCCUACGCC GCGACGAGUA GGAGGGCCGC UGCGGUGAGC CUUGAAGCCU AGGGCGCGGG CCCGGGUGGA GCCGCCGCAG GUGCAGAUCU UGGUGGUAGU AGCAAAUAUU CAAACGAGAA CUUUGAAGGC CGAAGUGGAG AAGGGUUCCA UGUGAACAGC AGUUGAACAU GGGUCAGUCG GUCCUGAGAG AUGGGCGAGC GCCGUUCCGA AGGGACGGGC GAUGGCCUCC GUUGCCCUCG GCCGAUCGAA AGGGAGUCGG GUUCAGAUCC CCGAAUCCGG AGUGGCGGAG AUGGGCGCCG CGAGGCGUCC AGUGCGGUAA CGCGACCGAU CCCGGAGAAG CCGGCGGGAG CCCCGGGGAG AGUUCUCUUU UCUUUGUGAA GGGCAGGGCG CCCUGGAAUG GGUUCGCCCC GAGAGAGGGG CCCGUGCCUU GGAAAGCGUC GCGGUUCCGG CGGCGUCCGG UGAGCUCUCG CUGGCCCUUG AAAAUCCGGG GGAGAGGGUG UAAAUCUCGC GCCGGGCCGU ACCCAUAUCC GCAGCAGGUC UCCAAGGUGA ACAGCCUCUG GCAUGUUGGA ACAAUGUAGG UAAGGGAAGU CGGCAAGCCG GAUCCGUAAC UUCGGGAUAA GGAUUGGCUC UAAGGGCUGG CAGCCGACUU AGAACUGGUG CGGACCAGGG GAAUCCGACU GUUUAAUUAA AACAAAGCAU CGCGAAGGCC CGCGGCGGGU GUUGACGCGA UGUGAUUUCU GCCCAGUGCU CUGAAUGUCA AAGUGAAGAA AUUCAAUGAA GCGCGGGUAA ACGGCGGGAG UAACUAUGAC UCUCUUAAGG UAGCCAAAUG CCUCGUCAUC UAAUUAGUGA CGCGCAUGAA UGGAUGAACG AGAUUCCCAC UGUCCCUACC UACUAUCCAG CGAAACCACA GCCAAGGGAA CGGGCUUGGC GGAAUCAGCG GGGAAAGAAG ACCCUGUUGA GCUUGACUCU AGUCUGGCAC GGUGAAGAGA CAUGAGAGGU GUAGAAUAAG UGGGAGGCCC GGGCCGCCGG UGAAAUACCA CUACUCUGAU CGUUUUUUCA CUGACCCGGU GAGGCGGGGG GGCGAGCCCG AGGGGCUCUC GCUUCUGGCG CCAAGCGCCC GCCCGGCCGG GCGCGACCCG CUCCGGGGAC AGUGCCAGGU GGGGAGUUUG ACUGGGGCGG UACACCUGUC AAACGGUAAC GCAGGUGUCC UAAGGCGAGC UCAGGGAGGA CAGAAACCUC CCGUGGAGCA GAAGGGCAAA AGCUCGCUUG AUCUUGAUUU UCAGUACGAA UACAGACCGU GAAAGCGGGG CCUCACGAUC CUUCUGACCU UUUGGGUUUU AAGCAGGAGG UGUCAGAAAA GUUACCACAG GGAUAACUGG CUUGUGGCGG CCAAGCGUUC AUAGCGACGU CGCUUUUUGA UCCUUCGAUG UCGGCUCUUC CUAUCAUUGU GAAGCAGAAU UCGCCAAGCG UUGGAUUGUU CACCCACUAA UAGGGAACGU GAGCUGGGUU UAGACCGUCG UGAGACAGGU UAGUUUUACC CUACUGAUGA UGUGUUGUUG CCAUGGUAAU CCUGCUCAGU ACGAGAGGAA CCGCAGGUUC AGACAUUUGG UGUAUGUGCU UGGCUGAGGA GCCAAUGGGG CGAAGCUACC AUCUGUGGGA UUAUGACUGA ACGCCUCUAA GUCAGAAUCC CGCCCAGGCG GAACGAUACG GCAGCGCCGC GGAGCCUCGG UUGGCCUCGG AUAGCCGGUC CGGGGUCCGG UGCGGAGUGC CCUUCGUCCU GGGAAACGGG GCGCGGCCGG AAAGGCGGCC GCCCCCUCGC CCGUCACGCA CCGCACGUUC GUGGGGAACC UGGCGCUAAA CCAUUCGUAG ACGACCUGCU UCUGGGUCGG GGUUUCGUAC GUAGCAGAGC AGCUCCCUCG CUGCGAUCUA UUGAAAGUCA GCCCUCGACA CAAGGGUUUG UC
MassTheoretical: 1.170164875 MDa
SourceSpecies: Rabbit (rabbit)

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Component #6: nucleic-acid, ap/P-site tRNA

Nucleic-acidName: ap/P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUUCCGUAG UGUAGUGGUU AUCACGUUCG CCUAACACGC GAAAGGUCCC CGGUUCGAAA CCGGGCGGAA ACACCA
MassTheoretical: 24.437535 kDa
SourceSpecies: Rabbit (rabbit)

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Component #7: nucleic-acid, mRNA

Nucleic-acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUUCGUUAAA GA
MassTheoretical: 3.837328 kDa
SourceSpecies: Enterobacteria phage SP6 (bacteriophage)

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Component #8: nucleic-acid, pe/E-site-tRNA

Nucleic-acidName: pe/E-site-tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCGGACUUAG CUCAGUUGGG AGAGCGCCAG ACUGAAGAUC UGGAGGUCCU GUGUUCGAUC CACAGAGUUC GCACCA
MassTheoretical: 24.533586 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #9: nucleic-acid, 18S ribosomal RNA

Nucleic-acidName: 18S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UACCUGGUUG AUCCUGCCAG UAGCAUAUGC UUGUCUCAAA GAUUAAGCCA UGCAUGUCUA AGUACGCACG GCCGGUACAG UGAAACUGCG AAUGGCUCAU UAAAUCAGUU AUGGUUCCUU UGGUCGACUU GGAUAACUGU GGUAAUUCUA GAGCUAAUAC AUGCCGACGG GCGCUGACCC CCUUCGCGGG GGGGAUGCGU GCAUUUAUCA GAUCAAAACC AACCCGGGCU UUGGUGACUC UAGAUAACCU CGGGCCGAUC GCACGCCCCC CGUGGCGGCG ACGACCCAUU CGAACGUCUG CCCUAUCAAC UUUCGAUGGU AGUCGCCGUG CCUACCAUGG UGACCACGGG UGACGGGGAA UCAGGGUUCG AUUCCGGAGA GGGAGCCUGA GAAACGGCUA CCACAUCCAA GGAAGGCAGC AGGCGCGCAA AUUACCCACU CCCGACCCGG GGAGGUAGUG ACGAAAAAUA ACAAUACAGG ACUCUUUCGA GGCCCUGUAA UUGGAAUGAG UCCACUUUAA AUCCUUUAAC GAGGAUCCAU UGGAGGGCAA GUCUGGUGCC AGCAGCCGCG GUAAUUCCAG CUCCAAUAGC GUAUAUUAAA GUUGCUGCAG UUAAAAAGCU CGUAGUUGGA UCUUGGGAGC GGCCCCUUGC CUCUCGCCCG AAGCGUUUAC UUUGAAAAAA UUAGAGUGUU CAAAGCAGGC CCGAGCCGCC UGGAUACCGC AGCUAGGAAU AAUGGAAUAG GACCGCGGUU CUAUUUUGUU GGUUUUCGGA ACUGAGGCCA UGAUUAAGAG GGACGGCCGG GGGCAUUCGU AUUGCGCCGC UAGAGGUGAA AUUCUUGGAC CGGCGCAAGA CGGACCAGAG CGAAAGCAUU UGCCAAGAAU GUUUUCAUUA AUCAAGAACG AAAGUCGGAG GUUCGAAGAC GAUCAGAUAC CGUCGUAGUU CCGACCAUAA ACGAUGCCGA CCGGCGAUGC GGCGGCGUUA UUCCCAUGAC CCGCCGGGCA GCUUCCGGGA AACCAAAGUC UUUGGGUUCC GGGGGGAGUA UGGUUGCAAA GCUGAAACUU AAAGGAAUUG ACGGAAGGGC ACCACCAGGA GUGGAGCCUG CGGCUUAAUU UGACUCAACA CGGGAAACCU CACCCGGCCC GGACACGGAC AGGAUUGACA GAUUGAUAGC UCUUUCUCGA UUCCGUGGGU GGUGGUGCAU GGCCGUUCUU AGUUGGUGGA GCGAUUUGUC UGGUUAAUUC CGAUAACGAA CGAGACUCUG GCAUGCUAAC UAGUUACGCG ACCCCCGAGC GGUAACUUCU UAGAGGGACA AGUGGCGUUC AGCCACCCGA GAUUGAGCAA UAACAGGUCU GUGAUGCCCU UAGAUGUCCG GGGCUGCACG CGCGCUACAC UGACUGGCUC AGCGUGUGCC UACCCUACGC CGGCAGGCGC GGGUAACCCG UUGAACCCCA UUCGUGAUGG GGAUCGGGGA UUGCAAUUAU UCCCCAUGAA CGAGGAAUUC CCAGUAAGUG CGGGUCAUAA GCUUGCGUUG AUUAAGUCCC UGCCCUUUGU ACACACCGCC CGUCGCUACU ACCGAUUGGA UGGUUUAGUG AGGCCCUCGG AUCGGCCCCG CCGUGGCGGA GCGCUGAGAA GACGGUCGAA CUUGACUAUC UAGAGGAAGU AAAAGUCGUA ACAAGGUUUC CGUAGGUGAA CCUGCGGAAG GAUCAUUA
MassTheoretical: 551.108188 kDa
SourceSpecies: Rabbit (rabbit)

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Component #10: protein, ribosomal protein uS3

ProteinName: ribosomal protein uS3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.35759 kDa
SourceSpecies: Rabbit (rabbit)

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Component #11: protein, Ribosomal protein S5

ProteinName: Ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.424836 kDa
SourceSpecies: Rabbit (rabbit)

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Component #12: protein, ribosomal protein eS10

ProteinName: ribosomal protein eS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.773953 kDa
SourceSpecies: Rabbit (rabbit)

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Component #13: protein, 40S ribosomal protein S12

ProteinName: 40S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.393658 kDa
SourceSpecies: Rabbit (rabbit)

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Component #14: protein, ribosomal protein uS19

ProteinName: ribosomal protein uS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.273879 kDa
SourceSpecies: Rabbit (rabbit)

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Component #15: protein, ribosomal protein uS9

ProteinName: ribosomal protein uS9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.76548 kDa
SourceSpecies: Rabbit (rabbit)

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Component #16: protein, ribosomal protein eS17

ProteinName: ribosomal protein eS17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.447793 kDa
SourceSpecies: Rabbit (rabbit)

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Component #17: protein, ribosomal protein uS13

ProteinName: ribosomal protein uS13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.383064 kDa
SourceSpecies: Rabbit (rabbit)

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Component #18: protein, ribosomal protein eS19

ProteinName: ribosomal protein eS19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.822219 kDa
SourceSpecies: Rabbit (rabbit)

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Component #19: protein, ribosomal protein uS10

ProteinName: ribosomal protein uS10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.029072 kDa
SourceSpecies: Rabbit (rabbit)

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Component #20: protein, ribosomal protein eS25

ProteinName: ribosomal protein eS25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.801748 kDa
SourceSpecies: Rabbit (rabbit)

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Component #21: protein, Ribosomal protein S28

ProteinName: Ribosomal protein S28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.007069 kDa
SourceSpecies: Rabbit (rabbit)

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Component #22: protein, ribosomal protein uS14

ProteinName: ribosomal protein uS14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.12121 kDa
SourceSpecies: Rabbit (rabbit)

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Component #23: protein, Ribosomal protein S27a

ProteinName: Ribosomal protein S27aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.645277 kDa
SourceSpecies: Rabbit (rabbit)

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Component #24: protein, ribosomal protein RACK 1

ProteinName: ribosomal protein RACK 1Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.726164 kDa
SourceSpecies: Rabbit (rabbit)

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Component #25: protein, ribosomal protein uS2

ProteinName: ribosomal protein uS2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.24574 kDa
SourceSpecies: Rabbit (rabbit)

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Component #26: protein, 40S ribosomal protein S3a

ProteinName: 40S ribosomal protein S3a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.660012 kDa
SourceSpecies: Rabbit (rabbit)

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Component #27: protein, ribosomal protein uS5

ProteinName: ribosomal protein uS5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.574971 kDa
SourceSpecies: Rabbit (rabbit)

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Component #28: protein, ribosomal protein eS4

ProteinName: ribosomal protein eS4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.893043 kDa
SourceSpecies: Rabbit (rabbit)

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Component #29: protein, 40S ribosomal protein S6

ProteinName: 40S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.913867 kDa
SourceSpecies: Rabbit (rabbit)

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Component #30: protein, 40S ribosomal protein S7

ProteinName: 40S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.990465 kDa
SourceSpecies: Rabbit (rabbit)

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Component #31: protein, ribosomal protein eS8

ProteinName: ribosomal protein eS8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.132191 kDa
SourceSpecies: Rabbit (rabbit)

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Component #32: protein, Ribosomal protein S9 (Predicted)

ProteinName: Ribosomal protein S9 (Predicted)Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.222221 kDa
SourceSpecies: Rabbit (rabbit)

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Component #33: protein, Ribosomal protein S11

ProteinName: Ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.910176 kDa
SourceSpecies: Rabbit (rabbit)

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Component #34: protein, ribosomal protein uS15

ProteinName: ribosomal protein uS15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.057113 kDa
SourceSpecies: Rabbit (rabbit)

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Component #35: protein, ribosomal protein uS11

ProteinName: ribosomal protein uS11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.544659 kDa
SourceSpecies: Rabbit (rabbit)

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Component #36: protein, ribosomal protein eS21

ProteinName: ribosomal protein eS21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.863111 kDa
SourceSpecies: Rabbit (rabbit)

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Component #37: protein, Ribosomal protein S15a

ProteinName: Ribosomal protein S15aRibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.734357 kDa
SourceSpecies: Rabbit (rabbit)

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Component #38: protein, Ribosomal protein S23

ProteinName: Ribosomal protein S23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.626392 kDa
SourceSpecies: Rabbit (rabbit)

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Component #39: protein, ribosomal protein eS24

ProteinName: ribosomal protein eS24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.489176 kDa
SourceSpecies: Rabbit (rabbit)

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Component #40: protein, ribosomal protein eS26

ProteinName: ribosomal protein eS26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.087117 kDa
SourceSpecies: Rabbit (rabbit)

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Component #41: protein, ribosomal protein eS27

ProteinName: ribosomal protein eS27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.00057 kDa
SourceSpecies: Rabbit (rabbit)

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Component #42: protein, ribosomal protein eS30

ProteinName: ribosomal protein eS30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.239447 kDa
SourceSpecies: Rabbit (rabbit)

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Component #43: nucleic-acid, 5.8S ribosomal RNA

Nucleic-acidName: 5.8S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGACUCUUAG CGGUGGAUCA CUCGGCUCGU GCGUCGAUGA AGAACGCAGC UAGCUGCGAG AAUUAAUGUG AAUUGCAGGA CACAUUGAUC AUCGACACUU CGAACGCACU UGCGGCCCCG GGUUCCUCCC GGGGCUACGC CUGUCUGAGC GUCGCUU
MassTheoretical: 50.449812 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #44: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUCUACGGCC AUACCACCCU GAACGCGCCC GAUCUCGUCU GAUCUCGGAA GCUAAGCAGG GUCGGGCCUG GUUAGUACUU GGAUGGGAGA CCGCCUGGGA AUACCGGGUG CUGUAGGCU
MassTheoretical: 38.38575 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #45: protein, Ribosomal protein L8

ProteinName: Ribosomal protein L8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.456158 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #46: protein, ribosomal protein uL3

ProteinName: ribosomal protein uL3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.222949 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #47: protein, ribosomal protein uL4

ProteinName: ribosomal protein uL4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.171547 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #48: protein, ribosomal protein uL18

ProteinName: ribosomal protein uL18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.091371 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #49: protein, ribosomal protein eL6

ProteinName: ribosomal protein eL6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.262428 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #50: protein, ribosomal protein uL30

ProteinName: ribosomal protein uL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.733146 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #51: protein, ribosomal protein eL8

ProteinName: ribosomal protein eL8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.724568 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #52: protein, ribosomal protein uL6

ProteinName: ribosomal protein uL6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.770355 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #53: protein, Ribosomal protein L10 (Predicted)

ProteinName: Ribosomal protein L10 (Predicted)Ribosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.38176 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #54: protein, Ribosomal protein L11

ProteinName: Ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.270318 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #55: protein, ribosomal protein eL13

ProteinName: ribosomal protein eL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.574697 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #56: protein, ribosomal protein eL14

ProteinName: ribosomal protein eL14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.220309 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #57: protein, Ribosomal protein L15

ProteinName: Ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.076088 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #58: protein, ribosomal protein uL13

ProteinName: ribosomal protein uL13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.820395 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #59: protein, ribosomal protein uL22

ProteinName: ribosomal protein uL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.757627 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #60: protein, ribosomal protein eL18

ProteinName: ribosomal protein eL18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.556482 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #61: protein, ribosomal protein eL19

ProteinName: ribosomal protein eL19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.742146 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #62: protein, ribosomal protein eL20

ProteinName: ribosomal protein eL20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.66134 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #63: protein, ribosomal protein eL21

ProteinName: ribosomal protein eL21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.276518 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #64: protein, ribosomal protein eL22

ProteinName: ribosomal protein eL22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.481248 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #65: protein, Ribosomal protein L23

ProteinName: Ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.828295 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #66: protein, ribosomal protein eL24

ProteinName: ribosomal protein eL24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.087417 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #67: protein, ribosomal protein uL23

ProteinName: ribosomal protein uL23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.614023 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #68: protein, Ribosomal protein L26

ProteinName: Ribosomal protein L26 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.161899 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #69: protein, 60S ribosomal protein L27

ProteinName: 60S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.647584 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #70: protein, ribosomal protein uL15

ProteinName: ribosomal protein uL15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.47334 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #71: protein, ribosomal protein eL29

ProteinName: ribosomal protein eL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.996388 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #72: protein, ribosomal protein eL30

ProteinName: ribosomal protein eL30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.500556 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #73: protein, ribosomal protein eL31

ProteinName: ribosomal protein eL31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.506581 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #74: protein, ribosomal protein eL32

ProteinName: ribosomal protein eL32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.179215 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #75: protein, ribosomal protein eL33

ProteinName: ribosomal protein eL33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.433548 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #76: protein, ribosomal protein eL34

ProteinName: ribosomal protein eL34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.994621 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #77: protein, ribosomal protein uL29

ProteinName: ribosomal protein uL29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.462429 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #78: protein, ribosomal protein eL36

ProteinName: ribosomal protein eL36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.373708 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #79: protein, Ribosomal protein L37

ProteinName: Ribosomal protein L37 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.864596 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #80: protein, ribosomal protein eL38

ProteinName: ribosomal protein eL38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.107752 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #81: protein, ribosomal protein eL39

ProteinName: ribosomal protein eL39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.295562 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #82: protein, ribosomal protein eL40

ProteinName: ribosomal protein eL40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.957237 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #83: protein, ribosomal protein eL41

ProteinName: ribosomal protein eL41 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.473451 kDa
SourceSpecies: Oryctolagus cuniculus (rabbit)

+
Component #84: protein, ribosomal protein eL42

ProteinName: ribosomal protein eL42 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.345776 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #85: protein, ribosomal protein eL43

ProteinName: ribosomal protein eL43 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.168153 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #86: protein, ribosomal protein eL28

ProteinName: ribosomal protein eL28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.991366 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #87: protein, Ribosomal protein

ProteinName: Ribosomal protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.879422 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #88: protein, Ribosomal protein L12

ProteinName: Ribosomal protein L12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.290794 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #89: protein, ribosomal protein uL10

ProteinName: ribosomal protein uL10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.21784 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #90: protein, eukaryotic elongation factor 2 (eEF2)

ProteinName: eukaryotic elongation factor 2 (eEF2) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.056734 kDa
SourceSpecies: Rabbit (rabbit)

+
Component #91: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 327 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #92: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #93: ligand, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.522196 kDa

-
Experimental details

-
Sample preparation

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

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 32386
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

+
About Yorodumi

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