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- EMDB-53067: Cryo-EM structure of the A2085-methylated 50S ribosome of a MLSb ... -

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Basic information

Entry
Database: EMDB / ID: EMD-53067
TitleCryo-EM structure of the A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
Map dataPostprocessed map of the focused refinement of the large ribosomal subunit obtained after Multibody refinement in Relion
Sample
  • Complex: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
    • Protein or peptide: x 27 types
    • RNA: x 4 types
  • Ligand: x 5 types
KeywordsRIBOSOME
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. ...Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / : / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / : / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L24 / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L13, bacterial-type / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L2 signature. / Ribosomal protein L2, conserved site / : / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L5, C-terminal / ribosomal L5P family C-terminus / Ribosomal protein L5 / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L5 domain superfamily / Ribosomal protein L13 signature. / Ribosomal protein L13, conserved site
Similarity search - Domain/homology
Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 ...Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsRivalta A / Yonath A
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Life Sci Alliance / Year: 2025
Title: Structural studies on ribosomes of differentially macrolide-resistant strains.
Authors: André Rivalta / Aliza Fedorenko / Alexandre Le Scornet / Sophie Thompson / Yehuda Halfon / Elinor Breiner Goldstein / Sude Çavdaroglu / Tal Melenitzky / Disha-Gajanan Hiregange / Ella ...Authors: André Rivalta / Aliza Fedorenko / Alexandre Le Scornet / Sophie Thompson / Yehuda Halfon / Elinor Breiner Goldstein / Sude Çavdaroglu / Tal Melenitzky / Disha-Gajanan Hiregange / Ella Zimmerman / Anat Bashan / Mee-Ngan Frances Yap / Ada Yonath /
Abstract: Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily ...Antimicrobial resistance is a major global health challenge, diminishing the efficacy of many antibiotics, including macrolides. In , an opportunistic pathogen, macrolide resistance is primarily mediated by Erm-family methyltransferases, which mono- or dimethylate A2058 in the 23S ribosomal RNA, reducing drug binding. Although macrolide-ribosome interactions have been characterized in nonpathogenic species, their structural basis in clinically relevant pathogens remains limited. In this study, we investigate the impact of -mediated resistance on drug binding by analyzing ribosomes from strains with varying levels of expression and activity. Using cryo-electron microscopy, we determined the high-resolution structures of solithromycin-bound ribosomes, including those with dimethylated A2058. Our structural analysis reveals the specific interactions that enable solithromycin binding despite double methylation and resistance, as corroborated by microbiological and biochemical data, suggesting that further optimization of ketolide-ribosome interactions could enhance macrolide efficacy against resistant strains.
History
DepositionMar 10, 2025-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_53067.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the focused refinement of the large ribosomal subunit obtained after Multibody refinement in Relion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 440 pix.
= 362.56 Å
0.82 Å/pix.
x 440 pix.
= 362.56 Å
0.82 Å/pix.
x 440 pix.
= 362.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.1078327 - 0.29770273
Average (Standard dev.)0.0004785897 (±0.0058266413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 362.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 2 of the focused refinement of the large subunit

Fileemd_53067_half_map_1.map
AnnotationHalf-map 2 of the focused refinement of the large subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map 1 of the focused refinement of the large subunit

Fileemd_53067_half_map_2.map
AnnotationHalf-map 1 of the focused refinement of the large subunit
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : A2085-methylated 50S ribosome of a MLSb resistant S. aureus strai...

EntireName: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
Components
  • Complex: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
    • Protein or peptide: Large ribosomal subunit protein bL33A
    • Protein or peptide: Large ribosomal subunit protein bL34
    • Protein or peptide: Large ribosomal subunit protein bL35
    • Protein or peptide: Large ribosomal subunit protein bL36
    • Protein or peptide: Large ribosomal subunit protein bL17
    • RNA: 23S rRNA
    • RNA: 5S rRNA
    • Protein or peptide: Large ribosomal subunit protein uL2
    • Protein or peptide: Large ribosomal subunit protein uL3
    • Protein or peptide: Large ribosomal subunit protein uL4
    • Protein or peptide: Large ribosomal subunit protein uL5
    • Protein or peptide: Large ribosomal subunit protein uL6
    • Protein or peptide: Large ribosomal subunit protein uL13
    • Protein or peptide: Large ribosomal subunit protein uL14
    • Protein or peptide: Large ribosomal subunit protein uL15
    • Protein or peptide: Large ribosomal subunit protein uL16
    • Protein or peptide: Large ribosomal subunit protein uL18
    • Protein or peptide: Large ribosomal subunit protein bL19
    • Protein or peptide: Large ribosomal subunit protein bL20
    • Protein or peptide: Large ribosomal subunit protein bL21
    • Protein or peptide: Large ribosomal subunit protein uL22
    • Protein or peptide: Large ribosomal subunit protein uL23
    • Protein or peptide: Large ribosomal subunit protein uL24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: Large ribosomal subunit protein bL27
    • Protein or peptide: Large ribosomal subunit protein bL28
    • Protein or peptide: Large ribosomal subunit protein uL29
    • Protein or peptide: Large ribosomal subunit protein uL30
    • Protein or peptide: Large ribosomal subunit protein bL32
    • RNA: P_site tRNA
    • RNA: E_site tRNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strai...

SupramoleculeName: A2085-methylated 50S ribosome of a MLSb resistant S. aureus strain "MNY196" in complex with solithromycin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#31
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)

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Macromolecule #1: Large ribosomal subunit protein bL33A

MacromoleculeName: Large ribosomal subunit protein bL33A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 6.305343 KDa
SequenceString:
MFNVRVNVTL ACTECGDRNY ITTKNKRNNP ERIEMKKYCP RLNKYTLHRE TK

UniProtKB: Large ribosomal subunit protein bL33A

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Macromolecule #2: Large ribosomal subunit protein bL34

MacromoleculeName: Large ribosomal subunit protein bL34 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 5.454642 KDa
SequenceString:
MVKRTYQPNK RKHSKVHGFR KRMSTKNGRK VLARRRRKGR KVLSA

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #3: Large ribosomal subunit protein bL35

MacromoleculeName: Large ribosomal subunit protein bL35 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 7.722368 KDa
SequenceString:
MPKMKTHRGA AKRVKRTASG QLKRSRAFTS HLFANKSTKQ KRQLRKARLV SKSDMKRVKQ LLAYKK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #4: Large ribosomal subunit protein bL36

MacromoleculeName: Large ribosomal subunit protein bL36 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 4.318422 KDa
SequenceString:
MKVRPSVKPI CEKCKVIKRK GKVMVICENP KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #5: Large ribosomal subunit protein bL17

MacromoleculeName: Large ribosomal subunit protein bL17 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 13.771773 KDa
SequenceString:
MGYRKLGRTS DQRKAMLRDL ATSLIISERI ETTEARAKEV RSVVEKLITL GKKGDLASRR NAAKTLRNVE ILNEDETTQT ALQKLFGEI AERYTERQGG YTRILKQGPR RGDGAESVII ELV

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #8: Large ribosomal subunit protein uL2

MacromoleculeName: Large ribosomal subunit protein uL2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 30.217164 KDa
SequenceString: MAIKKYKPIT NGRRNMTSLD FAEITKTTPE KSLLKPLPKK AGRNNQGKLT VRHHGGGHKR QYRVIDFKRN KDGINAKVDS IQYDPNRSA NIALVVYADG EKRYIIAPKG LEVGQIVESG AEADIKVGNA LPLQNIPVGT VVHNIELKPG KGGQIARSAG A SAQVLGKE ...String:
MAIKKYKPIT NGRRNMTSLD FAEITKTTPE KSLLKPLPKK AGRNNQGKLT VRHHGGGHKR QYRVIDFKRN KDGINAKVDS IQYDPNRSA NIALVVYADG EKRYIIAPKG LEVGQIVESG AEADIKVGNA LPLQNIPVGT VVHNIELKPG KGGQIARSAG A SAQVLGKE GKYVLIRLRS GEVRMILSTC RATIGQVGNL QHELVNVGKA GRSRWKGIRP TVRGSVMNPN DHPHGGGEGR AP IGRPSPM SPWGKPTLGK KTRRGKKSSD KLIVRGRKKK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #9: Large ribosomal subunit protein uL3

MacromoleculeName: Large ribosomal subunit protein uL3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 23.760256 KDa
SequenceString: MTKGILGRKI GMTQVFGENG ELIPVTVVEA KENVVLQKKT VEVDGYNAIQ VGFEDKKAYK KDAKSNKYAN KPAEGHAKKA DAAPKRFIR EFRNVDVDAY EVGQEVSVDT FVAGDVIDVT GVSKGKGFQG AIKRHGQSRG PMSHGSHFHR APGSVGMASD A SRVFKGQK ...String:
MTKGILGRKI GMTQVFGENG ELIPVTVVEA KENVVLQKKT VEVDGYNAIQ VGFEDKKAYK KDAKSNKYAN KPAEGHAKKA DAAPKRFIR EFRNVDVDAY EVGQEVSVDT FVAGDVIDVT GVSKGKGFQG AIKRHGQSRG PMSHGSHFHR APGSVGMASD A SRVFKGQK MPGRMGGNTV TVQNLEVVQV DTENKVILVK GNVPGPKKGL VEIRTSIKKG NK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #10: Large ribosomal subunit protein uL4

MacromoleculeName: Large ribosomal subunit protein uL4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 22.495697 KDa
SequenceString: MANYDVLKLD GTKSGSIELS DAVFGIEPNN SVLFEAINLQ RASLRQGTHA VKNRSAVSGG GRKPWKQKGT GRARQGTIRA PQWRGGGIV FGPTPRSYAY KMPKKMRRLA LRSALSFKAQ ENGLTVVDAF NFEAPKTKEF KNVLSTLEQP KKVLVVTENE D VNVELSAR ...String:
MANYDVLKLD GTKSGSIELS DAVFGIEPNN SVLFEAINLQ RASLRQGTHA VKNRSAVSGG GRKPWKQKGT GRARQGTIRA PQWRGGGIV FGPTPRSYAY KMPKKMRRLA LRSALSFKAQ ENGLTVVDAF NFEAPKTKEF KNVLSTLEQP KKVLVVTENE D VNVELSAR NIPGVQVTTA QGLNVLDITN ADSLVITEAA AKKVEEVLG

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #11: Large ribosomal subunit protein uL5

MacromoleculeName: Large ribosomal subunit protein uL5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 20.296637 KDa
SequenceString:
MNRLKEKFNT EVTENLMKKF NYSSVMEVPK IDKIVVNMGV GDAVQNSKVL DNAVEELELI TGQKPLVTKA KKSIATFRLR EGMPIGAKV TLRGERMYEF LDKLISVSLP RVRDFQGVSK KAFDGRGNYT LGVKEQLIFP EIDYDKVSKV RGMDIVIVTT A NTDEEARE LLANFGMPFR K

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #12: Large ribosomal subunit protein uL6

MacromoleculeName: Large ribosomal subunit protein uL6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 19.81858 KDa
SequenceString:
MSRVGKKIID IPSDVTVTFD GNHVTVKGPK GELSRTLNER MTFKQEENTI EVVRPSDSKE DRTNHGTTRA LLNNMVQGVS QGYVKVLEL VGVGYRAQMQ GKDLILNVGY SHPVEIKAEE NITFSVEKNT VVKVEGISKE QVGALASNIR SVRPPEPYKG K GIRYQGEY VRRKEGKTGK

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #13: Large ribosomal subunit protein uL13

MacromoleculeName: Large ribosomal subunit protein uL13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 16.359427 KDa
SequenceString:
MRQTFMANES NIERKWYVID AEGQTLGRLS SEVASILRGK NKVTYTPHVD TGDYVIVINA SKIEFTGNKE TDKVYYRHSN HPGGIKSIT AGELRRTNPE RLIENSIKGM LPSTRLGEKQ GKKLFVYGGA EHPHAAQQPE NYELRG

UniProtKB: Large ribosomal subunit protein uL13

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Macromolecule #14: Large ribosomal subunit protein uL14

MacromoleculeName: Large ribosomal subunit protein uL14 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 13.157342 KDa
SequenceString:
MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKNATPGG VVKKGDVVKA VIVRTKSGVR RNDGSYIKFD ENACVIIRD DKGPRGTRIF GPVARELREG NFMKIVSLAP EVL

UniProtKB: Large ribosomal subunit protein uL14

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Macromolecule #15: Large ribosomal subunit protein uL15

MacromoleculeName: Large ribosomal subunit protein uL15 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 15.62889 KDa
SequenceString:
MKLHELKPAE GSRKERNRVG RGVATGNGKT SGRGHKGQKA RSGGGVRPGF EGGQLPLFRR LPKRGFTNIN RKEYAIVNLD QLNKFEDGT EVTPALLVES GVVKNEKSGI KILGNGSLDK KLTVKAHKFS ASAAEAIDAK GGAHEVI

UniProtKB: Large ribosomal subunit protein uL15

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Macromolecule #16: Large ribosomal subunit protein uL16

MacromoleculeName: Large ribosomal subunit protein uL16 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 16.274049 KDa
SequenceString:
MLLPKRVKYR RQHRPKTTGR SKGGNYVTFG EFGLQATTTS WITSRQIESA RIAMTRYMKR GGKVWIKIFP HTPYTKKPLE VRMGAGKGA VEGWIAVVKP GRILFEVAGV SEEVAREALR LASHKLPVKT KFVKREELGG ETNES

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #17: Large ribosomal subunit protein uL18

MacromoleculeName: Large ribosomal subunit protein uL18 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 13.124093 KDa
SequenceString:
MISKIDKNKV RLKRHARVRT NLSGTAEKPR LNVYRSNKHI YAQIIDDNKG VTLAQASSKD SDIATTATKV ELATKVGEAI AKKAADKGI KEIVFDRGGY LYHGRVKALA EAARESGLEF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #18: Large ribosomal subunit protein bL19

MacromoleculeName: Large ribosomal subunit protein bL19 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 13.392771 KDa
SequenceString:
MTNHKLIEAV TKSQLRTDLP SFRPGDTLRV HVRIIEGTRE RIQVFEGVVI KRRGGGVSET FTVRKISSGV GVERTFPLHT PKIEKIEVK RRGKVRRAKL YYLRSLRGKA ARIQEIR

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #19: Large ribosomal subunit protein bL20

MacromoleculeName: Large ribosomal subunit protein bL20 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 13.720295 KDa
SequenceString:
MPRVKGGTVT RARRKKTIKL AKGYFGSKHT LYKVAKQQVM KSGQYAFRDR RQRKRDFRKL WITRINAAAR QHEMSYSRLM NGLKKAGID INRKMLSEIA ISDEKAFAQL VTKAKDALK

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #20: Large ribosomal subunit protein bL21

MacromoleculeName: Large ribosomal subunit protein bL21 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 11.354081 KDa
SequenceString:
MFAIIETGGK QIKVEEGQEI FVEKLDVNEG DTFTFDKVLF VGGDSVKVGA PTVEGATVTA TVNKQGRGKK ITVFTYKRRK NSKRKKGHR QPYTKLTIDK INA

UniProtKB: Large ribosomal subunit protein bL21

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Macromolecule #21: Large ribosomal subunit protein uL22

MacromoleculeName: Large ribosomal subunit protein uL22 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 12.857922 KDa
SequenceString:
MEAKAVARTI RIAPRKVRLV LDLIRGKNAA EAIAILKLTN KASSPVIEKV LMSALANAEH NYDMNTDELV VKEAYANEGP TLKRFRPRA QGRASAINKR TSHITIVVSD GKEEAKEA

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #22: Large ribosomal subunit protein uL23

MacromoleculeName: Large ribosomal subunit protein uL23 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 10.625398 KDa
SequenceString:
MEARDILKRP VITEKSSEAM AEDKYTFDVD TRVNKTQVKM AVEEIFNVKV ASVNIMNYKP KKKRMGRYQG YTNKRRKAIV TLKEGSIDL FN

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #23: Large ribosomal subunit protein uL24

MacromoleculeName: Large ribosomal subunit protein uL24 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 11.561504 KDa
SequenceString:
MHIKKGDNVK VIAGKDKGKE GKVIATLPKK DRVVVEGVNI MKKHQKPTQL NPEGGILETE AAIHVSNVQL LDPKTNEPTR VGYKFVDGK KVRIAKKSGE EIKSNN

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #24: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 23.810609 KDa
SequenceString: MASLKSIIRQ GKQTRSDLKQ LRKSGKVPAV VYGYGTKNVS VKVDEVEFIK VIREVGRNGV IELGVGSKTI KVMVADYQFD PLKNQITHI DFLAINMSEE RTVEVPVQLV GEAVGAKEGG VVEQPLFNLE VTATPDNIPE AIEVDITELN INDSLTVADV K VTGDFKIE ...String:
MASLKSIIRQ GKQTRSDLKQ LRKSGKVPAV VYGYGTKNVS VKVDEVEFIK VIREVGRNGV IELGVGSKTI KVMVADYQFD PLKNQITHI DFLAINMSEE RTVEVPVQLV GEAVGAKEGG VVEQPLFNLE VTATPDNIPE AIEVDITELN INDSLTVADV K VTGDFKIE NDSAESVVTV VAPTEEPTEE EIEAMEGEQQ TEEPEVVGES KEDEEKTEE

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #25: Large ribosomal subunit protein bL27

MacromoleculeName: Large ribosomal subunit protein bL27 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 10.334798 KDa
SequenceString:
MLKLNLQFFA SKKGVSSTKN GRDSESKRLG AKRADGQFVT GGSILYRQRG TKIYPGENVG RGGDDTLFAK IDGVVKFERK GRDKKQVSV YAVAE

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #26: Large ribosomal subunit protein bL28

MacromoleculeName: Large ribosomal subunit protein bL28 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 6.995289 KDa
SequenceString:
MGKQCFVTGR KASTGNRRSH ALNSTKRRWN ANLQKVRILV DGKPKKVWVS ARALKSGKVT RV

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #27: Large ribosomal subunit protein uL29

MacromoleculeName: Large ribosomal subunit protein uL29 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 8.5929 KDa
SequenceString:
MVKQMKAKEI RDLTTSEIEE QIKSSKEELF NLRFQLATGQ LEETARIRTV RKTIARLKTV AREREIEQSK ANQ

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #28: Large ribosomal subunit protein uL30

MacromoleculeName: Large ribosomal subunit protein uL30 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 6.565683 KDa
SequenceString:
MAKLQITLTR SVIGRPETQR KTVEALGLKK TNSSVVVEDN PAIRGQINKV KHLVTVEEK

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #29: Large ribosomal subunit protein bL32

MacromoleculeName: Large ribosomal subunit protein bL32 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 6.500609 KDa
SequenceString:
MAVPKRRTSK TRKNKRRTHF KISVPGMTEC PNCGEYKLSH RVCKNCGSYN GEEVAAK

UniProtKB: Large ribosomal subunit protein bL32

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Macromolecule #6: 23S rRNA

MacromoleculeName: 23S rRNA / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 946.85075 KDa
SequenceString: GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGU AAGUAAGCUU UGAUCCAGAG AUUUCCGAAU GGGGAAACCC AGCAUGAGUU AUGUCAUGUU AUCGAUAUGU G AAUACAUA ...String:
GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGU AAGUAAGCUU UGAUCCAGAG AUUUCCGAAU GGGGAAACCC AGCAUGAGUU AUGUCAUGUU AUCGAUAUGU G AAUACAUA GCAUAUCAGA AGGCACACCC GGAGAACUGA AACAUCUUAG UACCCGGAGG AAGAGAAAGA AAAUUCGAUU CC CUUAGUA GCGGCGAGCG AAACGGGAAG AGCCCAAACC AACAAGCUUG CUUGUUGGGG UUGUAGGACA CUCUGUACGG AGU UACAAA GGACGACAUU AGACGAAUCA UCUGGAAAGA UGAAUCAAAG AAGGUAAUAA UCCUGUAGUC GAAAAUGUUG UCUC UCUUG AGUGGAUCCU GAGUACGACG GAGCACGUGA AAUUCCGUCG GAAUCUGGGA GGACCAUCUC CUAAGGCUAA AUACU CUCU AGUGACCGAU AGUGAACCAG UACCGUGAGG GAAAGGUGAA AAGCACCCCG GAAGGGGAGU GAAAUAGAAC CUGAAA CCG UGUGCUUACA AGUAGUCAGA GCCCGUUAAU GGGUGAUGGC GUGCCUUUUG UAGAAUGAAC CGGCGAGUUA CGAUUUG AU GCAAGGUUAA GCAGUAAAUG UGGAGCCGUA GCGAAAGCGA GUCUGAAUAG GGCGUUUAGU AUUUGGUCGU AGACCCGA A ACCAGGUGAU CUACCCUUGG UCAGGUUGAA GUUCAGGUAA CACUGAAUGG AGGACCGAAC CGACUUACGU (5MU)GAAA AGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGG GCU AGCCUCAAGU GAUGAUUAUU GGAGGUAGAG CACUGUUUGG ACGAGGGGCC CCUCUCGGGU UACCGAAUUC AGACAAA CU CCGAAUGCCA AUUAAUUUAA CUUGGGAGUC AGAACAUGGG UGAUAAGGUC CGUGUUCGAA AGGGAAACAG CCCAGACC A CCAGCUAAGG UCCCAAAAUA UAUGUUAAGU GGAAAAGGAU GUGGCGUUGC CCAGACAACU AGGAUGUUGG CUUAGAAGC AGCCAUCAUU UAAAGAGUGC GUAAUAGCUC ACUAGUCGAG UGACACUGCG CCGAAAAUGU ACCGGGGCUA AACAUAUUAC CGAAGCUGU GGAUUGUCCU UUGGACAAUG GUAGGAGAGC GUUCUAAGGG CGUUGAAGCA UGAUCGUAAG GACAUGUGGA G CGCUUAGA AGUGAGAAUG CCGGUGUGAG UAGCGAAAGA CGGGUGAGAA UCCCGUCCAC CGAUUGACUA AGGUUUCCAG AG GAAGGCU CGUCCGCUCU GGGUUAGUCG GGUCCUAAGC UGAGGCCGAC AGGCGUAGGC GAUGGAUAAC AGGUUGAUAU UCC UGUACC ACCUAUAAUC GUUUUAAUCG AUGGGGGGAC GCAGUAGGAU AGGCGAAGCG UGCGAUUGGA UUGCACGUCU AAGC AGUAA GGCUGAGUAU UAGGCAAAUC CGGUACUCGU UAAGGCUGAG CUGUGAUGGG GAGAAGACAU UGAGUCUUCG AGUCG UUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGA GAA UUCUAAGGUG AGCGAGCGAA CUCUCGUUAA GGAACUCGGC AAAAUGACCC CGUAACUUCG GGAGAAGGGG UGCUCUU UA GGGUUAACGC CCAGAAGAGC CGCAGUGAAU AGGCCCAAGC GACUGUUUAU CAAAAACACA GGUCUCUGCU AAACCGUA A GGUGAUGUAU AGGGGCUGAC GCCUGCCCGG UGCUGGAAGG UUAAGAGGAG UGGUUAGCUU CUGCGAAGCU ACGAAUCGA AGCCCCAGUA AACGGCGGCC GUAACUAUAA CGGUCCUAAG GUAGCGAAA(5MU) UCCUUGUCGG GUAAGUUCCG ACCCGC ACG AAAGGCGUAA CGAUUUGGGC ACUGUCUCAA CGAGAGACUC GGUGAAAUCA UAGUACCUGU GAAGAUGCAG GUUACCC GC GACAGGACGG (MA6)AAGACCCCG UGGAGCUUUA CUGUAGCCUG AUAUUGAAAU UCGGCACAGC UUGUACAGGA UAGG UAGGA GCCUUUGAAA CGUGAGCGCU AGCUUACGUG GAGGCGCUGG UGGGAUACUA CCCUAGCUGU GUUGGCUUUC UAACC CGCA CCACUUAUCG UGGUGGGAGA CAGUGUCAGG CGGGCAGUUU GACUG(OMG)GGCG GUCGCCUCCU AAAAGGUAAC GG AGGCGCU CAAAGGUUCC CUCAGAAUGG UUGGAAAUCA UUCAUAGAGU GUAAAGGCAU AAGGGAGCUU GACUGCGAGA CCU ACAAGU CGAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGC UACCC CG(2MG)GGA(H2U)AAC AGGC(PSU)UAUCU CCCCCAAGAG UUCACAUCGA CGGGGAGGUU UGGCACCUCG (2MA)UGUCGGCU CAUCGCAUCC UGGGGCUGUA GUCGGUCCCA AGGGUUGGGC UGUUCGCCCA UUAAAGCGGU AC(G7M) CGAGC(PSU) GGGUUCAGAA CGUCGUGAGA CAGU(PSU)CGGUC CCUAUCCGUC GUGGGCGUAG GAAAUUUGAG AGGAGC UGU CCUUAGUACG AGAGGACCGG GAUGGACAUA CCUCUGGUGU ACCAGUUGUC GUGCCAACGG CAUAGCUGGG UAGCUAU GU GUGGACGGGA UAAGUGCUGA AAGCAUCUAA GCAUGAAGCC CCCCUCAAGA UGAGAUUUCC CAACUUCGGU UAUAAGAU C CCUCAAAGAU GAUGAGGUUA AUAGGUUCGA GGUGGAAGCA UGGUGACAUG UGGAGCUGAC GAAUACUAAU CGAUCGAAG ACUUAAUCAA

+
Macromolecule #7: 5S rRNA

MacromoleculeName: 5S rRNA / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 36.974945 KDa
SequenceString:
UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGUCG AUGGUAGUCG AACUUACGU UCCGCUAGAG UAGAACGUUG CCAGGC

GENBANK: GENBANK: CP030384.1

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Macromolecule #30: P_site tRNA

MacromoleculeName: P_site tRNA / type: rna / ID: 30 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 22.969725 KDa
SequenceString:
CGCGGGAUGG AGCAGGAGCU CGUCGGGCUC AUAGGCCGAA GGCGGUGGUU CAAAUCCGCC UCCCGCAACC A

+
Macromolecule #31: E_site tRNA

MacromoleculeName: E_site tRNA / type: rna / ID: 31 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus subsp. aureus USA300 (bacteria)
Molecular weightTheoretical: 4.170574 KDa
SequenceString:
GGCCGGGCCA CCA

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Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #33: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 33 / Number of copies: 231 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #34: (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,...

MacromoleculeName: (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H- ...Name: (3aS,4R,7S,9R,10R,11R,13R,15R,15aR)-1-{4-[4-(3-aminophenyl)-1H-1,2,3-triazol-1-yl]butyl}-4-ethyl-7-fluoro-11-methoxy-3a ,7,9,11,13,15-hexamethyl-2,6,8,14-tetraoxotetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-10-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
type: ligand / ID: 34 / Number of copies: 1 / Formula: EM1
Molecular weightTheoretical: 845.009 Da

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Macromolecule #35: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 35 / Number of copies: 12 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #36: water

MacromoleculeName: water / type: ligand / ID: 36 / Number of copies: 665 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION
Details: Resolution refers to gold-standard FSC 0.143 cutoff calculated on the postprocessed, solvent mask map
Number images used: 263087
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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