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- EMDB-3493: Structure of the 70S ribosome (empty A site) -

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Basic information

Entry
Database: EMDB / ID: EMD-3493
TitleStructure of the 70S ribosome (empty A site)
Map data
SampleStructure of the 70S ribosome (empty A site):
(nucleic-acidNucleic acid) x 5 / (50S ribosomal protein ...) x 31 / (30S ribosomal protein ...) x 20 / (ligand) x 4
Function / homology
Function and homology information


mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / RNA folding / Group I intron splicing / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity ...mRNA binding involved in posttranscriptional gene silencing / stringent response / ornithine decarboxylase inhibitor activity / misfolded RNA binding / transcription antitermination factor activity, RNA binding / RNA folding / Group I intron splicing / endoribonuclease inhibitor activity / positive regulation of ribosome biogenesis / negative regulation of endoribonuclease activity / translation repressor activity / transcription antitermination / negative regulation of translational initiation / four-way junction DNA binding / mature ribosome assembly / translational initiation / translational termination / ribosome assembly / translation repressor activity, mRNA regulatory element binding / endodeoxyribonuclease activity / positive regulation of RNA splicing / polysomal ribosome / DNA-templated transcription, termination / assembly of large subunit precursor of preribosome / response to reactive oxygen species / positive regulation of translational fidelity / regulation of cell growth / maintenance of translational fidelity / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 5'-UTR binding / large ribosomal subunit rRNA binding / cytoplasmic translation / ribosome biogenesis / cytosolic large ribosomal subunit / large ribosomal subunit / ribosome binding / 5S rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / response to radiation / regulation of translation / regulation of mRNA stability / small ribosomal subunit / transferase activity / negative regulation of translation / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / mRNA binding / response to antibiotic / negative regulation of transcription, DNA-templated / RNA binding / zinc ion binding / membrane / cytosol
Ribosomal S11, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site ...Ribosomal S11, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein S4, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein L29, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein S13, conserved site / K homology domain-like, alpha/beta / Ribosomal protein S14, conserved site / Ribosomal protein S18, conserved site / Ribosomal protein S21, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein S17, conserved site / Ribosomal protein S13, bacterial-type / Ribosomal protein S11, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L2, domain 3 / Ribosomal protein L25, short-form / K homology domain superfamily, prokaryotic type / Ribosomal protein L15, bacterial-type / Ribosomal protein L20 / Ribosomal protein L13 / Ribosomal protein L13, bacterial-type / KOW / Ribosomal protein L24/L26, conserved site / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L30, bacterial-type / Ribosomal protein S12/S23 / Ribosomal protein L11, bacterial-type / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L2, domain 2 / S15/NS1, RNA-binding / Ribosomal protein S13-like, H2TH / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Zinc-binding ribosomal protein / Nucleic acid-binding, OB-fold / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L23/L15e core domain superfamily / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / Ribosomal protein S5, N-terminal / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein S7 domain superfamily / Ribosomal protein L20, C-terminal / Ribosomal protein S7 domain / Ribosomal protein S16 domain superfamily / Ribosomal protein L28/L24 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S10 domain / Ribosomal protein L31 type A / Ribosomal protein L21-like / Ribosomal protein L25 / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / Ribosomal protein L36 superfamily / Ribosomal protein S19, superfamily / Ribosomal protein S6 superfamily / Ribosomal protein S8 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal L18e/L15P superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S20 superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein L4 domain superfamily / Ribosomal protein L9, C-terminal / Ribosomal protein L5, conserved site / Ribosomal protein L9, N-terminal / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S16, conserved site / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein S7, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal
50S ribosomal protein L21 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 ...50S ribosomal protein L21 / 30S ribosomal protein S5 / 30S ribosomal protein S8 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L14 / 50S ribosomal protein L16 / 50S ribosomal protein L23 / 30S ribosomal protein S15 / 50S ribosomal protein L17 / 50S ribosomal protein L4 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 30S ribosomal protein S14 / 30S ribosomal protein S17 / 50S ribosomal protein L18 / 50S ribosomal protein L2 / 50S ribosomal protein L3 / 50S ribosomal protein L24 / 30S ribosomal protein S3 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 30S ribosomal protein S21 / 30S ribosomal protein S4 / 50S ribosomal protein L9 / 30S ribosomal protein S2 / 50S ribosomal protein L31 / 30S ribosomal protein S6 / 30S ribosomal protein S7 / 50S ribosomal protein L15 / 50S ribosomal protein L10 / 50S ribosomal protein L11 / 50S ribosomal protein L19 / 50S ribosomal protein L20 / 50S ribosomal protein L27 / 50S ribosomal protein L28 / 50S ribosomal protein L29 / 50S ribosomal protein L32 / 30S ribosomal protein S20 / 50S ribosomal protein L33 / 50S ribosomal protein L34 / 50S ribosomal protein L35 / 50S ribosomal protein L36 / 30S ribosomal protein S10 / 30S ribosomal protein S11 / 30S ribosomal protein S12 / 30S ribosomal protein S13 / 30S ribosomal protein S16 / 30S ribosomal protein S18 / 30S ribosomal protein S19 / 50S ribosomal protein L25
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsJames NR / Brown A / Gordiyenko Y / Ramakrishnan V
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
CitationJournal: Science / Year: 2016
Title: Translational termination without a stop codon.
Authors: Nathan R James / Alan Brown / Yuliya Gordiyenko / V Ramakrishnan /
Abstract: Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA) ...Ribosomes stall when they encounter the end of messenger RNA (mRNA) without an in-frame stop codon. In bacteria, these "nonstop" complexes can be rescued by alternative ribosome-rescue factor A (ArfA). We used electron cryomicroscopy to determine structures of ArfA bound to the ribosome with 3'-truncated mRNA, at resolutions ranging from 3.0 to 3.4 angstroms. ArfA binds within the ribosomal mRNA channel and substitutes for the absent stop codon in the A site by specifically recruiting release factor 2 (RF2), initially in a compact preaccommodated state. A similar conformation of RF2 may occur on stop codons, suggesting a general mechanism for release-factor-mediated translational termination in which a conformational switch leads to peptide release only when the appropriate signal is present in the A site.
Validation ReportPDB-ID: 5mdz

SummaryFull reportAbout validation report
History
DepositionNov 13, 2016-
Header (metadata) releaseDec 14, 2016-
Map releaseDec 14, 2016-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mdz
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3493.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å
1.04 Å/pix.
x 400 pix.
= 416. Å
1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy EMDB: 0.06 / Movie #1: 0.07
Minimum - Maximum-0.53110796 - 0.9419762
Average (Standard dev.)0.0019713955 (±0.027926428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ224224224
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.5310.9420.002

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Supplemental data

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Half map: #1

Fileemd_3493_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_3493_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Structure of the 70S ribosome (empty A site)

EntireName: Structure of the 70S ribosome (empty A site) / Number of components: 61

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Component #1: protein, Structure of the 70S ribosome (empty A site)

ProteinName: Structure of the 70S ribosome (empty A site) / Recombinant expression: No
MassTheoretical: 2 MDa

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Component #2: nucleic-acid, 23S ribosomal RNA

nucleic acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU ...Sequence:
GGUUAAGCGA CUAAGCGUAC ACGGUGGAUG CCCUGGCAGU CAGAGGCGAU GAAGGACGUG CUAAUCUGCG AUAAGCGUCG GUAAGGUGAU AUGAACCGUU AUAACCGGCG AUUUCCGAAU GGGGAAACCC AGUGUGUUUC GACACACUAU CAUUAACUGA AUCCAUAGGU UAAUGAGGCG AACCGGGGGA ACUGAAACAU CUAAGUACCC CGAGGAAAAG AAAUCAACCG AGAUUCCCCC AGUAGCGGCG AGCGAACGGG GAGCAGCCCA GAGCCUGAAU CAGUGUGUGU GUUAGUGGAA GCGUCUGGAA AGGCGCGCGA UACAGGGUGA CAGCCCCGUA CACAAAAAUG CACAUGCUGU GAGCUCGAUG AGUAGGGCGG GACACGUGGU AUCCUGUCUG AAUAUGGGGG GACCAUCCUC CAAGGCUAAA UACUCCUGAC UGACCGAUAG UGAACCAGUA CCGUGAGGGA AAGGCGAAAA GAACCCCGGC GAGGGGAGUG AAAAAGAACC UGAAACCGUG UACGUACAAG CAGUGGGAGC ACGCUUAGGC GUGUGACUGC GUACCUUUUG UAUAAUGGGU CAGCGACUUA UAUUCUGUAG CAAGGUUAAC CGAAUAGGGG AGCCGAAGGG AAACCGAGUC UUAACUGGGC GUUAAGUUGC AGGGUAUAGA CCCGAAACCC GGUGAUCUAG CCAUGGGCAG GUUGAAGGUU GGGUAACACU AACUGGAGGA CCGAACCGAC UAAU(1MG)(PSU)(5MU)GAA AAAUUAGCGG AUGACUUGUG GCUGGGGGUG AAAGGCCAAU CAAACCGGGA GAUAGCUGGU UCUCCCCGAA AGCUAUUUAG GUAGCGCCUC GUGAAUUCAU CUCCGGGGGU AGAGCACUGU UUCGGCAAGG GGGUCAACCC GACUUACCAA CCCGAUGCAA ACUGCGAAUA CCGGAGAAUG UUAUCACGGG AGACACACGG CGGG(PSU)GCUAA CGUCCGUCGU GAAGAGGGAA ACAACCCAGA CCGCCAGCUA AGGUCCCAAA GUCAUGGUUA AGUGGGAAAC GAUGUGGGAA GGCCCAGACA GCCAGGAUGU UGGCUUAGAA GCAGCCAUCA UUUAAAGAAA GCGUAAUAGC UCACUGGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAACCAUGC ACCGAAGCUG CGGCAGCGAC GCUUAUGCGU UGUUGGGUAG GGGAGCGUUC UGUAAGCCUG CGAAGGUGUG CUGUGAGGCA UGCUGGAGGU AUCAGAAGUG CGAAUGCUGA CAUAAGUAAC GAUAAAGCGG GUGAAAAGCC CGCUCGCCGG AAGACCAAGG GUUCCUGUCC AACGUUAAUC GGGGCAGGGU GAGUCGACCC CUAAGGCGAG GCCGAAAGGC GUAGUCGAUG GGAAACAGGU UAAUAUUCCU GUACUUGGUG UUACUGCGAA GGGGGGACGG AGAAGGCUAU GUUGGCCGGG CGACGGUUGU CCCGGUUUAA GCGUGUAGGC UGGUUUUCCA GGCAAAUCCG GAAAAUCAAG GCUGAGGCGU GAUGACGAGG CACUACGGUG CUGAAGCAAC AAAUGCCCUG CUUCCAGGAA AAGCCUCUAA GCAUCAGGUA ACAUCAAAUC GUACCCCAAA CCGACAC(6MZ)GG UGGUCAGGUA GAGAAUACCA AGGCGCUUGA GAGAACUCGG GUGAAGGAAC UAGGCAAAAU GGUGCCGUAA CUUCGGGAGA AGGCACGCUG AUAUGUAGGU GAGGUCCCUC GCGGAUGGAG CUGAAAUCAG UCGAAGAUAC CAGCUGGCUG CAACUGUUUA UUAAAAACAC AGCACUGUGC AAACACGAAA GUGGACGUAU ACGGUGUGAC GCCU(2MG)CCCGG UGCCGGAAGG UUAAUUGAUG GGGUUAGCGC AAGCGAAGCU CUUGAUCGAA GCCCCGGUAA ACGGCGGCCG (PSU)AAC(3TD)A(PSU)AAC GGUCCUAAGG UAGCGAAA(5MU)U CCUUGUCGGG UAAGUUCCGA C(5MC)UGCACGAA UGGCGUAAUG AUGGCCAGGC UGUCUCCACC CGAGACUCAG UGAAAUUGAA CUCGCUGUG(6MZ) AGAUGCAGUG UACCCGCGGC AAGACGGAAA GACCCCGU(G7M)A ACCUUUACUA UAGCUUGACA CUGAACAUUG AGCCUUGAUG UGUAGGAUAG GUGGGAGGCU UUGAAGUGUG GACGCCAGUC UGCAUGGAGC CGACCUUGAA AUACCACCCU UUAAUGUUUG AUGUUCUAAC GUUGACCCGU AAUCCGGGUU GCGGACAGUG UCUGGUGGGU AGUUUGACUG (OMG)GGCGGUCUC CUCCUAAAGA GUAACGGAGG AGCACGAAGG UUGGCUAAUC CUGGUCGGAC AUCAGGAGGU UAGUGCAAUG GCAUAAGCCA GCUUGACUGC GAGCGUGACG GCGCGAGCAG GUGCGAAAGC AGGUCAUAGU GAUCCGGUGG UUCUGAAUGG AAGGGCCAUC GCUCAACGGA UAAAAGGUAC UCCG(2MG)GGAUA ACAGGC(PSU)GAU ACCGCCCAAG AGUUCAUAUC GACGGCGGUG UUUGGCA(OMC)CU CG(2MA)(PSU)GUCGGC UCAUCACAUC CUGGGGCUGA AGUAGGUCCC AAGGGUAUGG C(OMU)GUUCGCCA UUUAAAGUGG UACGCGAGC(PSU) GGGUUUAGAA CGUCGUGAGA CAGU(PSU)CGGUC CCUAUCUGCC GUGGGCGCUG GAGAACUGAG GGGGGCUGCU CCUAGUACGA GAGGACCGGA GUGGACGCAU CACUGGUGUU CGGGUUGUCA UGCCAAUGGC ACUGCCCGGU AGCUAAAUGC GGAAGAGAUA AGUGCUGAAA GCAUCUAAGC ACGAAACUUG CCCCGAGAUG AGUUCUCCCU GACCCUUUAA GGGUCCUGAA GGAACGUUGA AGACGACGAC GUUGAUAGGC CGGGUGUGUA AGCGCAGCGA UGCGUUGAGC UAACCGGUAC UAAUGAACCG UGAGGCUUAA CCUU
MassTheoretical: 941.832625 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: nucleic-acid, 16S ribosomal RNA

nucleic acidName: 16S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU ...Sequence:
AAAUUGAAGA GUUUGAUCAU GGCUCAGAUU GAACGCUGGC GGCAGGCCUA ACACAUGCAA GUCGAACGGU AACAGGAAGA AGCUUGCUUC UUUGCUGACG AGUGGCGGAC GGGUGAGUAA UGUCUGGGAA ACUGCCUGAU GGAGGGGGAU AACUACUGGA AACGGUAGCU AAUACCGCAU AACGUCGCAA GACCAAAGAG GGGGACCUUC GGGCCUCUUG CCAUCGGAUG UGCCCAGAUG GGAUUAGCUA GUAGGUGGGG UAACGGCUCA CCUAGGCGAC GAUCCCUAGC UGGUCUGAGA GGAUGACCAG CCACACUGGA ACUGAGACAC GGUCCAGACU CCUACGGGAG GCAGCAGUGG GGAAUAUUGC ACAAUGGGCG CAAGCCUGAU GCAGCCAUGC CGCGUGUAUG AAGAAGGCCU UCGGGUUGUA AAGUACUUUC AGCGGGGAGG AAGGGAGUAA AGUUAAUACC UUUGCUCAUU GACGUUACCC GCAGAAGAAG CACCGGCUAA CUCCG(PSU)GCCA GCAGCC(7MG)CGG UAAUACGGAG GGUGCAAGCG UUAAUCGGAA UUACUGGGCG UAAAGCGCAC GCAGGCGGUU UGUUAAGUCA GAUGUGAAAU CCCCGGGCUC AACCUGGGAA CUGCAUCUGA UACUGGCAAG CUUGAGUCUC GUAGAGGGGG GUAGAAUUCC AGGUGUAGCG GUGAAAUGCG UAGAGAUCUG GAGGAAUACC GGUGGCGAAG GCGGCCCCCU GGACGAAGAC UGACGCUCAG GUGCGAAAGC GUGGGGAGCA AACAGGAUUA GAUACCCUGG UAGUCCACGC CGUAAACGAU GUCGACUUGG AGGUUGUGCC CUUGAGGCGU GGCUUCCGGA GCUAACGCGU UAAGUCGACC GCCUGGGGAG UACGGCCGCA AGGUUAAAAC UCAAAUGAAU UGACGGGGGC CCGCACAAGC GGUGGAGCAU GUGGUUUAAU UCGAU(2MG)(5MC)AAC GCGAAGAACC UUACCUGGUC UUGACAUCCA CGGAAGUUUU CAGAGAUGAG AAUGUGCCUU CGGGAACCGU GAGACAGGUG CUGCAUGGCU GUCGUCAGCU CGUGUUGUGA AAUGUUGGGU UAAGUCCCGC AACGAGCGCA ACCCUUAUCC UUUGUUGCCA GCGGUCCGGC CGGGAACUCA AAGGAGACUG CCAGUGAUAA ACUGGAGGAA GGUGGGGAUG ACGUCAAGUC AUCAUG(2MG)CCC UUACGACCAG GGCUACACAC GUGCUACAAU GGCGCAUACA AAGAGAAGCG ACCUCGCGAG AGCAAGCGGA CCUCAUAAAG UGCGUCGUAG UCCGGAUUGG AGUCUGCAAC UCGACUCCAU GAAGUCGGAA UCGCUAGUAA UCGUGGAUCA GAAUGCCACG GUGAAUACGU UCCCGGGCCU UGUACACACC G(4OC)CCGU(5MC)ACA CCAUGGGAGU GGGUUGCAAA AGAAGUAGGU AGCUUAACCU UCGGGAGGGC GCUUACCACU UUGUGAUUCA UGACUGGGGU GAAGUCG(UR3)AA CAAGGUAACC GUAGG(2MG)G(MA6)(MA6)C CUGCGGUUGG AUCA
MassTheoretical: 497.405969 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: nucleic-acid, 5S ribosomal RNA

nucleic acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCAU
MassTheoretical: 38.79009 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #5: nucleic-acid, mRNA

nucleic acidName: mRNAMessenger RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCAAGGAGG UAAAAAUG
MassTheoretical: 5.922644 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #6: nucleic-acid, fMet-NH-tRNA(fMet)

nucleic acidName: fMet-NH-tRNA(fMet) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGGGGU(4SU)G AGCAGCCUGG (H2U)AGCUCGUCG GG(4OC)UCAUAAC CCGAAGAUCG UCGG(5MU)(PSU)CAAA UCCGGCCCCC GCAACC(8AN)(FME)
MassTheoretical: 24.966127 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #7: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.923619 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #8: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.277535 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #9: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.121566 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #10: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.333611 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #11: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.932791 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #12: protein, 50S ribosomal protein L9

ProteinName: 50S ribosomal protein L9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.78902 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #13: protein, 50S ribosomal protein L10

ProteinName: 50S ribosomal protein L10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.736596 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #14: protein, 50S ribosomal protein L11

ProteinName: 50S ribosomal protein L11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.894362 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #15: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.050606 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #16: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.565067 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #17: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.008471 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #18: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.312269 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #19: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.393657 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #20: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.794668 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #21: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.159278 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #22: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.528024 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #23: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.586374 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #24: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.253359 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #25: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.22216 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #26: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.33925 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #27: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.713465 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #28: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.14654 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #29: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.027551 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #30: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.286464 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #31: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.55482 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #32: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.887117 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #33: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.463445 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #34: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.388631 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #35: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.397463 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #36: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.313032 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #37: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.37739 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #38: protein, 30S ribosomal protein S2

ProteinName: 30S ribosomal protein S2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.78167 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #39: protein, 30S ribosomal protein S3

ProteinName: 30S ribosomal protein S3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.031316 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #40: protein, 30S ribosomal protein S4

ProteinName: 30S ribosomal protein S4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.514199 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #41: protein, 30S ribosomal protein S5

ProteinName: 30S ribosomal protein S5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.629398 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #42: protein, 30S ribosomal protein S6

ProteinName: 30S ribosomal protein S6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.727512 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #43: protein, 30S ribosomal protein S7

ProteinName: 30S ribosomal protein S7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.055156 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #44: protein, 30S ribosomal protein S8

ProteinName: 30S ribosomal protein S8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.146557 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #45: protein, 30S ribosomal protein S9

ProteinName: 30S ribosomal protein S9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.88627 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #46: protein, 30S ribosomal protein S10

ProteinName: 30S ribosomal protein S10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.755597 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #47: protein, 30S ribosomal protein S11

ProteinName: 30S ribosomal protein S11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.870975 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #48: protein, 30S ribosomal protein S12

ProteinName: 30S ribosomal protein S12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.814249 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #49: protein, 30S ribosomal protein S13

ProteinName: 30S ribosomal protein S13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.128467 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #50: protein, 30S ribosomal protein S14

ProteinName: 30S ribosomal protein S14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.60656 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #51: protein, 30S ribosomal protein S15

ProteinName: 30S ribosomal protein S15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.290816 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #52: protein, 30S ribosomal protein S16

ProteinName: 30S ribosomal protein S16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.207572 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #53: protein, 30S ribosomal protein S17

ProteinName: 30S ribosomal protein S17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.724491 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #54: protein, 30S ribosomal protein S18

ProteinName: 30S ribosomal protein S18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.005472 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #55: protein, 30S ribosomal protein S19

ProteinName: 30S ribosomal protein S19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.455355 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #56: protein, 30S ribosomal protein S20

ProteinName: 30S ribosomal protein S20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.708464 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #57: protein, 30S ribosomal protein S21

ProteinName: 30S ribosomal protein S21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.524039 kDa
SourceSpecies: Escherichia coli (E. coli)

+
Component #58: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 437 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #59: ligand, N-FORMYLMETHIONINE

LigandName: N-FORMYLMETHIONINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.177221 kDa

+
Component #60: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #61: ligand, water

LigandName: water / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 134615.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 140027
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL / Overall bvalue: 75.3
Output model

+
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