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- EMDB-0202: Cryo-EM structure of the ribosome-NatA complex -

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Basic information

Entry
Database: EMDB / ID: 0202
TitleCryo-EM structure of the ribosome-NatA complex
Map dataRibosome-NatA complex aligned on the ribosome and filtered according to local resolution.
SampleRibosome-NatA complex
  • 60S ribosomal subunit
  • N-terminal acetyl transferase A
  • (nucleic-acidNucleic acid) x 5
  • (60S ribosomal protein ...) x 40
  • Ubiquitin-60S ribosomal protein L40
  • ribosomal protein RPL1
  • (N-terminal acetyltransferase A complex ...) x 2
  • N-alpha-acetyltransferase NAT5
  • nascent polypeptide chain
  • ligand
Function / homologyRibosomal protein L38e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta 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 L36e domain superfamily ...Ribosomal protein L38e superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L6, alpha-beta 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 L36e domain superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L22e superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L40e superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L35A superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L30/YlxQ / 60S ribosomal protein L19 / Ribosomal protein L14 / Ribosomal protein L7/L30 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ubiquitin family / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L6 / Ribosomal protein L32e superfamily / Ribosomal protein L29/L35 superfamily / Ribosomal protein L13 / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Ribosomal protein L18e, conserved site / 60S ribosomal protein L18a/ L20, eukaryotes / N-terminal acetyltransferase A, auxiliary subunit / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L30e, conserved site / Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L24e, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L19/L19e superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L19/L19e conserved site / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / 50S ribosomal protein L30e-like / Ubiquitin-like domain superfamily / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L19, eukaryotic / Ribosomal protein L7, eukaryotic/archaeal / KOW motif / Ribosomal protein L4/L1 family / Ribosomal protein L21e signature. / Ribosomal protein L30 signature. / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 signature. / Ribosomal protein L23 signature. / Ribosomal protein L39e signature. / Ubiquitin domain signature. / Ribosomal protein L5 signature. / Ribosomal protein L22 signature. / Ribosomal protein L2 signature. / Ribosomal protein L3 signature. / Ribosomal protein L15 signature. / Ribosomal protein L19e signature. / Ribosomal protein L29 signature. / Ribosomal protein L32e signature. / Ribosomal protein L6 signature 2. / Ribosomal proteins L26 eukaryotic, L24P archaeal / Ribosomal protein L30e signature 1. / Ribosomal protein L13 signature. / Ribosomal protein L1e signature. / Ribosomal protein L30e signature 2. / Ribosomal protein L24e signature. / Ribosomal protein L37e signature. / Ribosomal protein L7Ae signature. / Ribosomal protein L13e signature. / Ribosomal protein L35Ae signature. / Ribosomal protein L18e signature. / Ribosomal protein L27e signature. / Ribosomal protein L24 signature. / Ribosomal protein L31e signature. / Ribosomal protein L34e signature. / Ribosomal protein 60S L18 and 50S L18e / 60S ribosomal protein L4 C-terminal domain
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsKnorr AG / Becker T / Berninghausen O / Beckmann R
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.
Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann
Validation ReportPDB-ID: 6hd7

SummaryFull reportAbout validation report
DateDeposition: Aug 17, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Dec 19, 2018 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
  • Map surface with fitted models
  • Surface level: 0.0126
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0202.map.gz (map file in CCP4 format, 296353 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
420 pix
1.08 Å/pix.
= 455.28 Å
420 pix
1.08 Å/pix.
= 455.28 Å
420 pix
1.08 Å/pix.
= 455.28 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:0.0126 (by author), 0.0126 (movie #1):
Minimum - Maximum-0.0984338 - 0.22589912
Average (Standard dev.)0.00047320456 (0.008901068)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions420420420
Origin0.00.00.0
Limit419.0419.0419.0
Spacing420420420
CellA=B=C: 455.28 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/z420420420
origin x/y/z0.0000.0000.000
length x/y/z455.280455.280455.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.0980.2260.000

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Supplemental data

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Sample components

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Entire Ribosome-NatA complex

EntireName: Ribosome-NatA complex
Details: Coordinates are only deposited for 60S subunit and NatA.
Number of components: 55

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Component #1: protein, Ribosome-NatA complex

ProteinName: Ribosome-NatA complex
Details: Coordinates are only deposited for 60S subunit and NatA.
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, 60S ribosomal subunit

ProteinName: 60S ribosomal subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, N-terminal acetyl transferase A

ProteinName: N-terminal acetyl transferase A / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #4: nucleic-acid, Saccharomyces cerevisiae S288C 35S pre-ribosomal RN...

Nucleic-acidName: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA
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)

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Component #5: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA5S 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)

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Component #6: nucleic-acid, 5.8S rRNA

Nucleic-acidName: 5.8S rRNA5.8S 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)

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Component #7: nucleic-acid, tRNA

Nucleic-acidName: tRNATransfer RNA / Class: RNA
Details: The A-site tRNA was modeled based on an E. coli tRNA-Lys
Structure: OTHER / Synthetic: No
Sequence:
GGGUCGUUAG CUCAGUUGGU AGAGCAGUUG ACUUUUAAUC AAUUGGUCGC AGGUUCGAAU CCUGCACGAC CCACCA
MassTheoretical: 24.378408 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #8: nucleic-acid, P-site tRNA

Nucleic-acidName: P-site tRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGAGCGGUAG UUCAGUCGGU UAGAAUACCU GCCUGUCACG CAGGGGGUCG CGGGUUCGAG UCCCGUCCGU UCCGCCA
MassTheoretical: 24.815684 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #9: protein, 60S ribosomal protein L42-A

ProteinName: 60S ribosomal protein L42-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.246658 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #10: protein, 60S ribosomal protein L43-A

ProteinName: 60S ribosomal protein L43-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.112952 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #11: protein, 60S ribosomal protein L2-A

ProteinName: 60S ribosomal protein L2-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.463574 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #12: protein, 60S ribosomal protein L3

ProteinName: 60S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.850793 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #13: protein, 60S ribosomal protein L4-A

ProteinName: 60S ribosomal protein L4-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.159125 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #14: protein, 60S ribosomal protein L5

ProteinName: 60S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.764828 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #15: protein, 60S ribosomal protein L6-A

ProteinName: 60S ribosomal protein L6-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.000564 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #16: protein, 60S ribosomal protein L7-A

ProteinName: 60S ribosomal protein L7-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.686281 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #17: protein, 60S ribosomal protein L8-A

ProteinName: 60S ribosomal protein L8-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.17582 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #18: protein, 60S ribosomal protein L9-A

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

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Component #19: protein, 60S ribosomal protein L11-A

ProteinName: 60S ribosomal protein L11-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.755691 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #20: protein, 60S ribosomal protein L13-A

ProteinName: 60S ribosomal protein L13-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.604164 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #21: protein, 60S ribosomal protein L14-A

ProteinName: 60S ribosomal protein L14-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.195066 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #22: protein, 60S ribosomal protein L15-A

ProteinName: 60S ribosomal protein L15-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.482357 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #23: protein, 60S ribosomal protein L16-A

ProteinName: 60S ribosomal protein L16-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.247227 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #24: protein, 60S ribosomal protein L17-A

ProteinName: 60S ribosomal protein L17-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.589518 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #25: protein, 60S ribosomal protein L18-A

ProteinName: 60S ribosomal protein L18-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.609252 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #26: protein, 60S ribosomal protein L19-A

ProteinName: 60S ribosomal protein L19-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.762316 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #27: protein, 60S ribosomal protein L20-A

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

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Component #28: protein, 60S ribosomal protein L21-A

ProteinName: 60S ribosomal protein L21-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.279266 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #29: protein, 60S ribosomal protein L22-A

ProteinName: 60S ribosomal protein L22-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.711359 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #30: protein, 60S ribosomal protein L23-A

ProteinName: 60S ribosomal protein L23-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.49395 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #31: protein, 60S ribosomal protein L24-A

ProteinName: 60S ribosomal protein L24-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.661717 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #32: protein, 60S ribosomal protein L25

ProteinName: 60S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.787612 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #33: protein, 60S ribosomal protein L26-A

ProteinName: 60S ribosomal protein L26-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.265784 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #34: protein, 60S ribosomal protein L27-A

ProteinName: 60S ribosomal protein L27-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.56836 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #35: protein, 60S ribosomal protein L28

ProteinName: 60S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.761666 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #36: protein, 60S ribosomal protein L29

ProteinName: 60S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.691884 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #37: protein, 60S ribosomal protein L30

ProteinName: 60S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.430364 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #38: protein, 60S ribosomal protein L31-A

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

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Component #39: protein, 60S ribosomal protein L32

ProteinName: 60S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.809441 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #40: protein, 60S ribosomal protein L33-A

ProteinName: 60S ribosomal protein L33-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.17713 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #41: protein, 60S ribosomal protein L34-A

ProteinName: 60S ribosomal protein L34-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.673196 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #42: protein, 60S ribosomal protein L35-A

ProteinName: 60S ribosomal protein L35-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.94264 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #43: protein, 60S ribosomal protein L36-A

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

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Component #44: protein, 60S ribosomal protein L37-A

ProteinName: 60S ribosomal protein L37-ARibosome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.877395 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #45: protein, 60S ribosomal protein L38

ProteinName: 60S ribosomal protein L38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.845561 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #46: protein, 60S ribosomal protein L39

ProteinName: 60S ribosomal protein L39 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.35864 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #47: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.583077 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #48: protein, 60S ribosomal protein L41-A

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

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Component #49: protein, ribosomal protein RPL1

ProteinName: ribosomal protein RPL1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.889996 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #50: protein, 60S ribosomal protein L10

ProteinName: 60S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.410465 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #51: protein, N-terminal acetyltransferase A complex subunit NAT1

ProteinName: N-terminal acetyltransferase A complex subunit NAT1 / Details: ribosome binding subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 99.050133 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #52: protein, N-terminal acetyltransferase A complex catalytic subunit ARD1

ProteinName: N-terminal acetyltransferase A complex catalytic subunit ARD1
Details: catalytic subunitCatalysis / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.635168 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #53: protein, N-alpha-acetyltransferase NAT5

ProteinName: N-alpha-acetyltransferase NAT5 / Details: ribosome binding subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.753727 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #54: protein, nascent polypeptide chain

ProteinName: nascent polypeptide chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.975426 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #55: ligand, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hyd...

LigandName: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.281347 kDa

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Experimental details

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Sample preparation

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

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 262507
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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