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- EMDB-10077: Erythromycin Resistant Staphylococcus aureus 50S ribosome (delta ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10077
TitleErythromycin Resistant Staphylococcus aureus 50S ribosome (delta R88 A89 uL22) in complex with erythromycin.
Map data
Sample
  • Complex: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
    • RNA: x 2 types
    • Protein or peptide: x 28 types
  • Ligand: x 1 types
KeywordsRibosome / antibiotics / resistance / Staphylococcus aureus / exit tunnel / RNA / rProteins / erythromycin
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 / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 ...Ribosomal protein L31 type B / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / : / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / : / Ribosomal protein L16 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / 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 L28/L24 superfamily / Ribosomal protein L32p, bacterial type / 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 L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, 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 L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / 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 L17 / Ribosomal protein L32p / 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 L24 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein L13, bacterial-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / 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 L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L15, conserved site / Ribosomal protein L15 signature.
Similarity search - Domain/homology
Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL33 ...Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L32 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsHalfon Y / Matozv D
Funding support Denmark, 2 items
OrganizationGrant numberCountry
European Research Council322581
Danish National Research Foundation Denmark
CitationJournal: Sci Rep / Year: 2019
Title: Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.
Authors: Yehuda Halfon / Donna Matzov / Zohar Eyal / Anat Bashan / Ella Zimmerman / Jette Kjeldgaard / Hanne Ingmer / Ada Yonath /
Abstract: The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit ...The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.
History
DepositionJun 18, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s0z
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10077.png

Downloads & links

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Map

FileDownload / File: emd_10077.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.)
1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å		1.07 Å/pix.
x 400 pix.
= 426.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.12392809 - 0.29235694
Average (Standard dev.)0.00021022212 (±0.0051371767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0671.0671.067
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.800426.800426.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1240.2920.000

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Supplemental data

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Sample components

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Entire : Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta ...

EntireName: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
Components
  • Complex: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
    • RNA: 23S ribosomal RNA
    • RNA: 5S ribosomal RNA
    • Protein or peptide: 50S ribosomal protein L2
    • Protein or peptide: 50S ribosomal protein L3
    • Protein or peptide: 50S ribosomal protein L4
    • Protein or peptide: 50S ribosomal protein L5
    • Protein or peptide: 50S ribosomal protein L6
    • Protein or peptide: 50S ribosomal protein L13
    • Protein or peptide: 50S ribosomal protein L14
    • Protein or peptide: 50S ribosomal protein L15
    • Protein or peptide: 50S ribosomal protein L16
    • Protein or peptide: 50S ribosomal protein L17
    • Protein or peptide: 50S ribosomal protein L18
    • Protein or peptide: 50S ribosomal protein L19
    • Protein or peptide: 50S ribosomal protein L20
    • Protein or peptide: 50S ribosomal protein L21
    • Protein or peptide: 50S ribosomal protein L22
    • Protein or peptide: 50S ribosomal protein L23
    • Protein or peptide: 50S ribosomal protein L24
    • Protein or peptide: 50S ribosomal protein L25
    • Protein or peptide: 50S ribosomal protein L27
    • Protein or peptide: 50S ribosomal protein L28
    • Protein or peptide: 50S ribosomal protein L29
    • Protein or peptide: 50S ribosomal protein L30
    • Protein or peptide: 50S ribosomal protein L31 type B
    • Protein or peptide: 50S ribosomal protein L32
    • Protein or peptide: 50S ribosomal protein L33
    • Protein or peptide: 50S ribosomal protein L34
    • Protein or peptide: 50S ribosomal protein L35
    • Protein or peptide: 50S ribosomal protein L36
  • Ligand: ERYTHROMYCIN A

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Supramolecule #1: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta ...

SupramoleculeName: Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22) in complex with erythromycin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#30
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: 23S ribosomal RNA

MacromoleculeName: 23S ribosomal RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 940.976 KDa
SequenceString: UUAAGUUAUU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG AAGCCGAUGA AGGACGUUAC UAACGACGAU AUGCUUUGGG GAGCUGUAA GUAAGCUUUG AUCCAGAGAU UUCCGAAUGG GGAAACCCAG CAUGAGUUAU GUCAUGUUAU CGAUAUGUGA A UACAUAGC ...String:
UUAAGUUAUU AAGGGCGCAC GGUGGAUGCC UUGGCACUAG AAGCCGAUGA AGGACGUUAC UAACGACGAU AUGCUUUGGG GAGCUGUAA GUAAGCUUUG AUCCAGAGAU UUCCGAAUGG GGAAACCCAG CAUGAGUUAU GUCAUGUUAU CGAUAUGUGA A UACAUAGC AUAUCAGAAG GCACACCCGG AGAACUGAAA CAUCUUAGUA CCCGGAGGAA GAGAAAGAAA AUUCGAUUCC CU UAGUAGC GGCGAGCGAA AUGGGAAGAG CCCAAACCAA CAAGCUUGCU UGUUGGGGUU GUAGGACACU CUACGGAGUU ACA AAGGAC GACAUUAGAC GAAUCAUCUG GAAAGAUGAA UCAAAGAAGG UAAUAAUCCU GUAGUCGAAA AUGUUGUCUC UCUU GAGUG GAUCCUGAGU ACGACGGAGC ACGUGAAAUU CCGUCGGAAU CUGGGAGGAC CAUCUCCUAA GGCUAAAUAC UCUCU AGUG ACCGAUAGUG AACCAGUACC GUGAGGGAAA GGUGAAAAGC ACCCCGGAAG GGGAGUGAAA UAGAACCUGA AACCGU GUG CUUACAAGUA GUCAGAGCCC GUUAAUGGGU GAUGGCGUGC CUUUUGUAGA AUGAACCGGC GAGUUACGAU UUGAUGC AA GGUUAAGCAG UAAAUGUGGA GCCGUAGCGA AAGCGAGUCU GAAUAGGGCG UUUAGUAUUU GGUCGUAGAC CCGAAACC A GGUGAUCUAC CCUUGGUCAG GUUGAAGUUC AGGUAACACU GAAUGGAGGA CCGAACCGAC UUACGUUGAA AAGUGAGCG GAUGAACUGA GGGUAGCGGA GAAAUUCCAA UCGAACCUGG AGAUAGCUGG UUCUCUCCGA AAUAGCUUUA GGGCUAGCCU CAAGUGAUG AUUAUUGGAG GUAGAGCACU GUUUGGACGA GGGGCCGGUU ACCGAAUUCA GACAAACUCC GAAUGCCAAU U AAUUUAAC UUGGGAGUCA GAACAUGGGU GAUAAGGUCC GUGUUCGAAA GGGAAACAGC CCAGACCACC AGCUAAGGUC CC AAAAUAU AUGUUAAGUG GAAAAGGAUG UGGCGUUGCC CAGACAACUA GGAUGUUGGC UUAGAAGCAG CCAUCAUUUA AAG AGUGCG UAAUAGCUCA CUAGUCGAGU GACACUGCGC CGAAAAUGUA CCGGGGCUAA ACAUAUUACC GAAGCUGUGG AUUG UCCUU UGGACAAUGG UAGGAGAGCG UUCUAAGGGC GUUGAAGCAU GAUCGUAAGG ACAUGUGGAG CGCUUAGAAG UGAGA AUGC CGGUGUGAGU AGCGAAAGAC GGGUGAGAAU CCCGUCCACC GAUUGACUAA GGUUUCCAGA GGAAGGCUCG UCCGCU CUG GGUUAGUCGG GUCCUAAGCU GAGGCCGACA GGCGUAGGCG AUGGAUAACA GGUUGAUAUU CCUGUACCAC CUAUAAU CG UUUUAAUCGA UGGGGGGACG CAGUAGGAUA GGCGAAGCGU GCGAUUGGAU UGCACGUCUA AGCAGUAAGG CUGAGUAU U AGGCAAAUCC GGUACUCGUU AAGGCUGAGC UGUGAUGGGG AGAAGACAUU GUGUCUUCGA GUCGUUGAUU UCACACUGC CGAGAAAAGC CUCUAGAUAG AAAAUAGGUG CCCGUACCGC AAACCGACAC AGGUAGUCAA GAUGAGAAUU CUAAGGUGAG CGAGCGAAC UCUCGUUAAG GAACUCGGCA AAAUGACCCC GUAACUUCGG GAGAAGGGGU GCUCUUUAGG GUUAACGCCC A GAAGAGCC GCAGUGAAUA GGCCCAAGCG ACUGUUUAUC AAAAACACAG GUCUCUGCUA AACCGUAAGG UGAUGUAUAG GG GCUGACG CCUGCCCGGU GCUGGAAGGU UAAGAGGAGU GGUUAGCUUC UGCGAAGCUA CGAAUCGAAG CCCCAGUAAA CGG CGGCCG UAUAACGGUC CUAAGGUAGC GAAAUUCCUU GUCGGGUAAG UUCCGACCCG CACGAAAGGC GUAACGAUUU GGGC ACUGU CUCAACGAGA GACUCGGUGA AAUCAUAGUA CCUGUGAAGA UGCAGGUUAC CCGCGACAGG ACGGAAAGAC CCCGU GGAG CUUUACUGUA GCCUGAUAUU GAAAUUCGGC ACAGCUUGUA CAGGAUAGGU AGGAGCCUUU GAAACGUGAG CGCUAG CUU ACGUGGAGGC GCUGGUGGGA UACUACCCUA GCUGUGUUGG CUUUCUAACC CGCACCACUU AUCGUGGUGG GAGACAG UG UCAGGCGGGC AGUUUGACUG GGGCGGUCGC CUCCUAAAAG GUAACGGAGG CGCUCAAAGG UUCCCUCAGA AUGGUUGG A AAUCAUUCAU AGAGUGUAAA GGCAUAAGGG AGCUUGACUG CGAGACCUAC AAGUCGAGCA GGGUCGAAAG ACGGACUUA GUGAUCCGGU GGUUCCGCAU GGAAGGGCCA UCGCUCAACG GAUAAAAGCU ACCCCGGGGA UAACAGGCUU AUCUCCCCCA AGAGUUCAC AUCGACGGGG AGGUUUGGCA CCUCGAUGUC GGCUCAUCGC AUCCUGGGGC UGUAGUCGGU CCCAAGGGUU G GGCUGUUC GCCCAUUAAA GCGGUACGCG AGCUGGGUUC AGAACGUCGU GAGACAGUUC GGUCCCUAUC CGUCGUGGGC GU AGGAAAU UUGAGAGGAG CUGUCCUUAG UACGAGAGGA CCGGGAUGGA CAUACCUCUG GUGUACCAGU UGUCGUGCCA ACG GCAUAG CUGGGUAGCU AUGUGUGGAC GGGAUAAGUG CUGAAAGCAU CUAAGCAUGA AGCCCCCCUC AAGAUGAGAU UUCC CAACU UCGGUUAUAA GAUCCCUCAA AGAUGAUGAG GUUAAUAGGU UCGAGGUGGA AGCAUGGUGA CAUGUGGAGC UGACG AAUA CUAAUCGAUC GAAGACUUAA U

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Macromolecule #2: 5S ribosomal RNA

MacromoleculeName: 5S ribosomal RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 36.669766 KDa
SequenceString:
UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGUCG AUGGUAGUCG AACUUACGU UCCGCUAGAG UAGAACGUUG CCAGG

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Macromolecule #3: 50S ribosomal protein L2

MacromoleculeName: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 29.827607 KDa
SequenceString: AIKKYKPITN GRRNMTSLDF AEITKTTPEK SLLKPLPKKA GRNNQGKLTV RHHGGGHKRQ YRVIDFKRNK DGINAKVDSI QYDPNRSAN IALVVYADGE KRYIIAPKGL EVGQIVESGA EADIKVGNAL PLQNIPVGTV VHNIELKPGK GGQIARSAGA S AQVLGKEG ...String:
AIKKYKPITN GRRNMTSLDF AEITKTTPEK SLLKPLPKKA GRNNQGKLTV RHHGGGHKRQ YRVIDFKRNK DGINAKVDSI QYDPNRSAN IALVVYADGE KRYIIAPKGL EVGQIVESGA EADIKVGNAL PLQNIPVGTV VHNIELKPGK GGQIARSAGA S AQVLGKEG KYVLIRLRSG EVRMILSTCR ATIGQVGNLQ HELVNVGKAG RSRWKGIRPT VRGSVMNPND HPHGGGEGRA PI GRPSPMS PWGKPTLGKK TRRGKKSSDK LIVRGRK

UniProtKB: Large ribosomal subunit protein uL2

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Macromolecule #4: 50S ribosomal protein L3

MacromoleculeName: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 23.199545 KDa
SequenceString: TKGILGRKIG MTQVFGENGE LIPVTVVEAK ENVVLQKKTV EVDGYNAIQV GFEDKKAYKK DAKSNKYANK PAEGHAKKAD AAPKRFIRE FRNVDVDAYE VGQEVSVDTF VAGDVIDVTG VSKGKGFQGA IKRHGQSRGP MSHGSHFHRA PGSVGMASDA S RVFKGQKM ...String:
TKGILGRKIG MTQVFGENGE LIPVTVVEAK ENVVLQKKTV EVDGYNAIQV GFEDKKAYKK DAKSNKYANK PAEGHAKKAD AAPKRFIRE FRNVDVDAYE VGQEVSVDTF VAGDVIDVTG VSKGKGFQGA IKRHGQSRGP MSHGSHFHRA PGSVGMASDA S RVFKGQKM PGRMGGNTVT VQNLEVVQVD TENKVILVKG NVPGPKKGLV EIRTSIK

UniProtKB: Large ribosomal subunit protein uL3

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Macromolecule #5: 50S ribosomal protein L4

MacromoleculeName: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 22.364504 KDa
SequenceString: ANYDVLKLDG TKSGSIELSD AVFGIEPNNS VLFEAINLQR ASLRQGTHAV KNRSAVSGGG RKPWKQKGTG RARQGTIRAP QWRGGGIVF GPTPRSYAYK MPKKMRRLAL RSALSFKAQE NGLTVVDAFN FEAPKTKEFK NVLSTLEQPK KVLVVTENED V NVELSARN ...String:
ANYDVLKLDG TKSGSIELSD AVFGIEPNNS VLFEAINLQR ASLRQGTHAV KNRSAVSGGG RKPWKQKGTG RARQGTIRAP QWRGGGIVF GPTPRSYAYK MPKKMRRLAL RSALSFKAQE NGLTVVDAFN FEAPKTKEFK NVLSTLEQPK KVLVVTENED V NVELSARN IPGVQVTTAQ GLNVLDITNA DSLVITEAAA KKVEEVLG

UniProtKB: Large ribosomal subunit protein uL4

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Macromolecule #6: 50S ribosomal protein L5

MacromoleculeName: 50S ribosomal protein L5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 19.460596 KDa
SequenceString:
LKEKFNTEVT ENLMKKFNYS SVMEVPKIDK IVVNMGVGDA VQNSKVLDNA VEELELITGQ KPLVTKAKKS IATFRLREGM PIGAKVTLR GERMYEFLDK LISVSLPRVR DFQGVSKKAF DGRGNYTLGV KEQLIFPEID YDKVSKVRGM DIVIVTTANT D EEARELLA NFGMP

UniProtKB: Large ribosomal subunit protein uL5

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Macromolecule #7: 50S ribosomal protein L6

MacromoleculeName: 50S ribosomal protein L6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 19.270869 KDa
SequenceString:
SRVGKKIIDI PSDVTVTFDG NHVTVKGPKG ELSRTLNERM TFKQEENTIE VVRPSDSKED RTNHGTTRAL LNNMVQGVSQ GYVKVLELV GVGYRAQMQG KDLILNVGYS HPVEIKAEEN ITFSVEKNTV VKVEGISKEQ VGALASNIRS VRPPEPYKGK G IRYQGEYV RRKEG

UniProtKB: Large ribosomal subunit protein uL6

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Macromolecule #8: 50S ribosomal protein L13

MacromoleculeName: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (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 #9: 50S ribosomal protein L14

MacromoleculeName: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (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 #10: 50S ribosomal protein L15

MacromoleculeName: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (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 #11: 50S ribosomal protein L16

MacromoleculeName: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 15.599435 KDa
SequenceString:
MLLPKRVKYR RQHRPKTTGR SKGGNYVTFG EFGLQATTTS WITSRQIESA RIAMTRYMKR GGKVWIKIFP HTPYTKKPLE VRMGAGKGA VEGWIAVVKP GRILFEVAGV SEEVAREALR LASHKLPVKT KFVKREEL

UniProtKB: Large ribosomal subunit protein uL16

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Macromolecule #12: 50S ribosomal protein L17

MacromoleculeName: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 13.583523 KDa
SequenceString:
YRKLGRTSDQ RKAMLRDLAT SLIISERIET TEARAKEVRS VVEKLITLGK KGDLASRRNA AKTLRNVEIL NEDETTQTAL QKLFGEIAE RYTERQGGYT RILKQGPRRG DGAESVIIEL V

UniProtKB: Large ribosomal subunit protein bL17

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Macromolecule #13: 50S ribosomal protein L18

MacromoleculeName: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 12.992897 KDa
SequenceString:
ISKIDKNKVR LKRHARVRTN LSGTAEKPRL NVYRSNKHIY AQIIDDNKGV TLAQASSKDS DIATTATKVE LATKVGEAIA KKAADKGIK EIVFDRGGYL YHGRVKALAE AARESGLEF

UniProtKB: Large ribosomal subunit protein uL18

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Macromolecule #14: 50S ribosomal protein L19

MacromoleculeName: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 13.104381 KDa
SequenceString:
TNHKLIEAVT KSQLRTDLPS FRPGDTLRVH VRIIEGTRER IQVFEGVVIK RRGGGVSETF TVRKISSGVG VERTFPLHTP KIEKIEVKR RGKVRRAKLY YLRSLRGKAA RIQEI

UniProtKB: Large ribosomal subunit protein bL19

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Macromolecule #15: 50S ribosomal protein L20

MacromoleculeName: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 13.459919 KDa
SequenceString:
PRVKGGTVTR ARRKKTIKLA KGYFGSKHTL YKVAKQQVMK SGQYAFRDRR QRKRDFRKLW ITRINAAARQ HEMSYSRLMN GLKKAGIDI NRKMLSEIAI SDEKAFAQLV TKAKDAL

UniProtKB: Large ribosomal subunit protein bL20

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Macromolecule #16: 50S ribosomal protein L21

MacromoleculeName: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (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 #17: 50S ribosomal protein L22

MacromoleculeName: 50S ribosomal protein L22 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 12.100087 KDa
SequenceString:
MEAKAVARTI RIAPRKVRLV LDLIRGKNAA EAIAILKLTN KASSPVIEKV LMSALANAEH NYDMNTDELV VKEAYANEGP TLKRFRPQG RASAINKRTS HITIVVSDGK E

UniProtKB: Large ribosomal subunit protein uL22

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Macromolecule #18: 50S ribosomal protein L23

MacromoleculeName: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 10.3801 KDa
SequenceString:
EARDILKRPV ITEKSSEAMA EDKYTFDVDT RVNKTQVKMA VEEIFNVKVA SVNIMNYKPK KKRMGRYQGY TNKRRKAIVT LKEGSIDLF

UniProtKB: Large ribosomal subunit protein uL23

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Macromolecule #19: 50S ribosomal protein L24

MacromoleculeName: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 11.316205 KDa
SequenceString:
HIKKGDNVKV IAGKDKGKEG KVIATLPKKD RVVVEGVNIM KKHQKPTQLN PEGGILETEA AIHVSNVQLL DPKTNEPTRV GYKFVDGKK VRIAKKSGEE IKSN

UniProtKB: Large ribosomal subunit protein uL24

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Macromolecule #20: 50S ribosomal protein L25

MacromoleculeName: 50S ribosomal protein L25 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 10.4622 KDa
SequenceString:
ASLKSIIRQG KQTRSDLKQL RKSGKVPAVV YGYGTKNVSV KVDEVEFIKV IREVGRNGVI ELGVGSKTIK VMVADYQFDP LKNQITHID FLAIN

UniProtKB: Large ribosomal subunit protein bL25

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Macromolecule #21: 50S ribosomal protein L27

MacromoleculeName: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 8.409478 KDa
SequenceString:
STKNGRDSES KRLGAKRADG QFVTGGSILY RQRGTKIYPG ENVGRGGDDT LFAKIDGVVK FERKGRDKKQ VSVYAVA

UniProtKB: Large ribosomal subunit protein bL27

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Macromolecule #22: 50S ribosomal protein L28

MacromoleculeName: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 5.499432 KDa
SequenceString:
ASTGNRRSHA LNSTKRRWNA NLQKVRILVD GKPKKVWVSA RALKSGKVT

UniProtKB: Large ribosomal subunit protein bL28

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Macromolecule #23: 50S ribosomal protein L29

MacromoleculeName: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 7.845942 KDa
SequenceString:
KAKEIRDLTT SEIEEQIKSS KEELFNLRFQ LATGQLEETA RIRTVRKTIA RLKTVARERE IEQSKAN

UniProtKB: Large ribosomal subunit protein uL29

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Macromolecule #24: 50S ribosomal protein L30

MacromoleculeName: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 6.434487 KDa
SequenceString:
AKLQITLTRS VIGRPETQRK TVEALGLKKT NSSVVVEDNP AIRGQINKVK HLVTVEEK

UniProtKB: Large ribosomal subunit protein uL30

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Macromolecule #25: 50S ribosomal protein L31 type B

MacromoleculeName: 50S ribosomal protein L31 type B / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 6.909694 KDa
SequenceString:
MKQGIHPEYH QVIFLDTTTN FKFLSGSTKT SSEMMEWEDG KEYPVIRLDI SSDSHPFYT

UniProtKB: Large ribosomal subunit protein bL31B

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Macromolecule #26: 50S ribosomal protein L32

MacromoleculeName: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 5.569565 KDa
SequenceString:
AVPKRRTSKT RKNKRRTHFK ISVPGMTECP NCGEYKLSHR VCKNCGSY

UniProtKB: 50S ribosomal protein L32

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Macromolecule #27: 50S ribosomal protein L33

MacromoleculeName: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 5.684561 KDa
SequenceString:
RVNVTLACTE CGDRNYITTK NKRNNPERIE MKKYCPRLNK YTLHRET

UniProtKB: Large ribosomal subunit protein bL33

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Macromolecule #28: 50S ribosomal protein L34

MacromoleculeName: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 5.252369 KDa
SequenceString:
VKRTYQPNKR KHSKVHGFRK RMSTKNGRKV LARRRRKGRK VLS

UniProtKB: Large ribosomal subunit protein bL34

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Macromolecule #29: 50S ribosomal protein L35

MacromoleculeName: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 7.461992 KDa
SequenceString:
PKMKTHRGAA KRVKRTASGQ LKRSRAFTSH LFANKSTKQK RQLRKARLVS KSDMKRVKQL LAYK

UniProtKB: Large ribosomal subunit protein bL35

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Macromolecule #30: 50S ribosomal protein L36

MacromoleculeName: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 4.318422 KDa
SequenceString:
MKVRPSVKPI CEKCKVIKRK GKVMVICENP KHKQRQG

UniProtKB: Large ribosomal subunit protein bL36

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Macromolecule #31: ERYTHROMYCIN A

MacromoleculeName: ERYTHROMYCIN A / type: ligand / ID: 31 / Number of copies: 1 / Formula: ERY
Molecular weightTheoretical: 733.927 Da
Chemical component information

ChemComp-ERY:
ERYTHROMYCIN A / antibiotic*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.076 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5ngm

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 378309
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT

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