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- EMDB-7870: Structure of the 50S ribosomal subunit from Methicillin Resistant... -

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Entry
Database: EMDB / Id: 7870
TitleStructure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6
Map data50S ribosomal subunit from MRSA in complex with an oxazolidinone antibiotic: LZD-6
Sample50S Ribosomal subunit from MRSA in complex with oxazolidinone LZD-5:
(50S ribosomal protein ...) x 25 / (nucleic-acidNucleic acid) x 2 / ligand
Func homologyRibosomal L18e/L15P superfamily / Ribosomal protein L36 signature. / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L10e/L16 superfamily ...Ribosomal L18e/L15P superfamily / Ribosomal protein L36 signature. / Ribosomal protein L22p/L17e / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L19 superfamily / Ribosomal protein L33 superfamily / Ribosomal protein L35 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25, C-terminal / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal protein L17 superfamily / L21-like superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L29/L35 superfamily / Ribosomal protein L36 superfamily / Ribosomal protein L20, C-terminal / L28p-like / Ribosomal protein L15 / Ribosomal protein L25 / Ribosomal protein L21-like / Ribosomal protein L28/L24 / Ribosomal protein L4 domain superfamily / Ribosomal protein L2, conserved site / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L35 / Ribosomal protein L14p/L23e / Ribosomal protein L23 / Ribosomal protein L34, conserved site / Ribosomal protein L19 / Ribosomal protein L16 signature 1. / Ribosomal protein L33 signature. / Ribosomal protein L15 signature. / Ribosomal protein L3 signature. / Ribosomal protein L2 signature. / Ribosomal protein L22 signature. / Ribosomal protein L14 signature. / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein TL5, C-terminal domain / Ribosomal Proteins L2, C-terminal domain / Ribosomal L32p protein family / Ribosomal protein L35 / Ribosomal L25p family / Ribosomal protein L17 / Ribosomal protein L3 / Ribosomal L27 protein / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal L29 protein / Ribosomal L28 family / Ribosomal prokaryotic L21 protein / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein L4/L1 family / Ribosomal protein L33 / Ribosomal protein L34 / KOW motif / Ribosomal protein L20 / Ribosomal protein L36 / Ribosomal protein L30p/L7e / Ribosomal protein L18e/L15P / Ribosomal protein L16, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L15, conserved site / Ribosomal protein L18, bacterial-type / Ribosomal protein L24 / Ribosomal protein L32p / Ribosomal protein L2 / Ribosomal protein L4/L1e / Ribosomal protein L19 / Ribosomal protein L29/L35 / Ribosomal protein L21 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L33 / Ribosomal protein L27 / Ribosomal protein L28 / Ribosomal protein L22/L17 / Ribosomal protein L25, beta domain / Ribosomal protein L25, long-form / Ribosomal protein L3 / Ribosomal protein L36 / Ribosomal protein L17 / Ribosomal protein L34 / Ribosomal protein L14P / Ribosomal protein L16 / Ribosomal protein L27 signature. / Ribosomal protein L35 signature. / Ribosomal protein L20 signature. / Ribosomal protein L19 signature. / Ribosomal protein L24 signature. / Ribosomal protein L17 signature. / Ribosomal protein L18 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L2, domain 2 / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L14P, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L3, conserved site
Function and homology information
SourceStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBelousoff MJ / Venugopal H / Bamert RS / Lithgow T
CitationJournal: ChemMedChem / Year: 2019
Title: cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.
P-authors: Matthew J Belousoff / Hari Venugopal / Alexander Wright / Samuel Seoner / Isabella Stuart / Chris Stubenrauch / Rebecca S Bamert / David W Lupton / Trevor Lithgow /
Abstract: While the ribosome is a common target for antibiotics, challenges with crystallography can impede the development of new bioactives using structure-based drug design approaches. In this study we ...While the ribosome is a common target for antibiotics, challenges with crystallography can impede the development of new bioactives using structure-based drug design approaches. In this study we exploit common structural features present in linezolid-resistant forms of both methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) to redesign the antibiotic. Enabled by rapid and facile cryoEM structures, this process has identified (S)-2,2-dichloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)acetamide (LZD-5) and (S)-2-chloro-N-((3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl) acetamide (LZD-6), which inhibit the ribosomal function and growth of linezolid-resistant MRSA and VRE. The strategy discussed highlights the potential for cryoEM to facilitate the development of novel bioactive materials.
Validation ReportPDB-ID: 6ddg

SummaryFull reportAbout validation report
DateDeposition: May 10, 2018 / Header (metadata) release: Jun 6, 2018 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: : PDB-6ddg
  • Surface level: 0.03
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_7870.map.gz (map file in CCP4 format, 192915 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
364 pix
1.06 Å/pix.
= 385.84 Å
364 pix
1.06 Å/pix.
= 385.84 Å
364 pix
1.06 Å/pix.
= 385.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.18029219 - 0.28413635
Average (Standard dev.)0.00061071455 (0.007736175)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions364364364
Origin0.00.00.0
Limit363.0363.0363.0
Spacing364364364
CellA=B=C: 385.83997 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z385.840385.840385.840
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.1800.2840.001

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Supplemental data

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Sample components

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Entire 50S Ribosomal subunit from MRSA in complex with oxazolidinone LZD-5

EntireName: 50S Ribosomal subunit from MRSA in complex with oxazolidinone LZD-5
Number of components: 29

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Component #1: protein, 50S Ribosomal subunit from MRSA in complex with oxazolid...

ProteinName: 50S Ribosomal subunit from MRSA in complex with oxazolidinone LZD-5
Recombinant expression: No
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #2: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.392771 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #3: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.087984 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #4: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.720295 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #5: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.354081 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #6: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.786844 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #7: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.625398 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #8: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.561504 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #9: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.810609 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #10: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.198369 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #11: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.995289 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #12: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.105266 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #13: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.459922 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #14: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.565683 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #15: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.500609 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #16: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.885783 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #17: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.454642 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #18: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.593188 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #19: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.318422 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #20: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.523752 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #21: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.359427 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #22: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.157342 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #23: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.62889 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #24: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.274049 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #25: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.771773 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #26: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.124093 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #27: nucleic-acid, 23S rRNA

Nucleic-acidName: 23S rRNA23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GAUUAAGUUA UUAAGGGCGC ACGGUGGAUG CCUUGGCACU AGAAGCCGAU GAAGGACGUU ACUAACGACG AUAUGCUUUG GGGAGCUGUA AGUAAGCUUU GAUCCAGAGA UUUCCGAAUG GGGAAACCCA GCAUGAGUUA UGUCAUGUUA UCGAUAUGUG AAUACAUAGC AUAUCAGAAG GCACACCCGG AGAACUGAAA CAUCUUAGUA CCCGGAGGAA GAGAAAGAAA AUUCGAUUCC CUUAGUAGCG GCGAGCGAAA CGGGAAGAGC CCAAACCAAC AAGCUUGCUU GUUGGGGUUG UAGGACACUC UAUACGGAGU UACAAAGGAC GACAUUAGAC GAAUCAUCUG GAAAGAUGAA UCAAAGAAGG UAAUAAUCCU GUAGUCGAAA AUGUUGUCUC UCUUGAGUGG AUCCUGAGUA CGACGGAGCA CGUGAAAUUC CGUCGGAAUC UGGGAGGACC AUCUCCUAAG GCUAAAUACU CUCUAGUGAC CGAUAGUGAA CCAGUACCGU GAGGGAAAGG UGAAAAGCAC CCCGGAAGGG GAGUGAAAUA GAACCUGAAA CCGUGUGCUU ACAAGUAGUC AGAGCCCGUU AAUGGGUGAU GGCGUGCCUU UUGUAGAAUG AACCGGCGAG UUACGAUUUG AUGCAAGGUU AAGCAGUAAA UGUGGAGCCG UAGCGAAAGC GAGUCUGAAU AGGGCGUUUA GUAUUUGGUC GUAGACCCGA AACCAGGUGA UCUACCCUUG GUCAGGUUGA AGUUCAGGUA ACACUGAAUG GAGGACCGAA CCGACUUACG UUGAAAAGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGGGCUA GCCUCAAGUG AUGAUUAUUG GAGGUAGAGC ACUGUUUGGA CGAGGGGCCC CUCUCGGGUU ACCGAAUUCA GACAAACUCC GAAUGCCAAU UAAUUUAACU UGGGAGUCAG AACAUGGGUG AUAAGGUCCG UGUUCGAAAG GGAAACAGCC CAGACCACCA GCUAAGGUCC CAAAAUAUAU GUUAAGUGGA AAAGGAUGUG GCGUUGCCCA GACAACUAGG AUGUUGGCUU AGAAGCAGCC AUCAUUUAAA GAGUGCGUAA UAGCUCACUA GUCGAGUGAC ACUGCGCCGA AAAUGUACCG GGGCUAAACA UAUUACCGAA GCUGUGGAUU GUCCUUUGGA CAAUGGUAGG AGAGCGUUCU AAGGGCGUUG AAGCAUGAUC GUAAGGACAU GUGGAGCGCU UAGAAGUGAG AAUGCCGGUG UGAGUAGCGA AAGACGGGUG AGAAUCCCGU CCACCGAUUG ACUAAGGUUU CCAGAGGAAG GCUCGUCCGC UCUGGGUUAG UCGGGUCCUA AGCUGAGGCC GACAGGCGUA GGCGAUGGAU AACAGGUUGA UAUUCCUGUA CCACCUAUAA UCGUUUUAAU CGAUGGGGGG ACGCAGUAGG AUAGGCGAAG CGUGCGAUUG GAUUGCACGU CUAAGCAGUA AGGCUGAGUA UUAGGCAAAU CCGGUACUCG UUAAGGCUGA GCUGUGAUGG GGAGAAGACA UUGUGUCUUC GAGUCGUUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGAGAAU UCUAAGGUGA GCGAGCGAAC UCUCGUUAAG GAACUCGGCA AAAUGACCCC GUAACUUCGG GAGAAGGGGU GCUCUUUAGG GUUAACGCCC AGAAGAGCCG CAGUGAAUAG GCCCAAGCGA CUGUUUAUCA AAAACACAGG UCUCUGCUAA ACCGUAAGGU GAUGUAUAGG GGCUGACGCC UGCCCGGUGC UGGAAGGUUA AGAGGAGUGG UUAGCUUCUG CGAAGCUACG AAUCGAAGCC CCAGUAAACG GCGGCCGUAA CUAUAACGGU CCUAAGGUAG CGAAAUUCCU UGUCGGGUAA GUUCCGACCC GCACGAAAGG CGUAACGAUU UGGGCACUGU CUCAACGAGA GACUCGGUGA AAUCAUAGUA CCUGUGAAGA UGCAGGUUAC CCGCGACAGG ACGGAAAGAC CCCGUGGAGC UUUACUGUAG CCUGAUAUUG AAAUUCGGCA CAGCUUGUAC AGGAUAGGUA GGAGCCUUUG AAACGUGAGC GCUAGCUUAC GUGGAGGCGC UGGUGGGAUA CUACCCUAGC UGUGUUGGCU UUCUAACCCG CACCACUUAU CGUGGUGGGA GACAGUGUCA GGCGGGCAGU UUGACUGGGG CGGUCGCCUC CUAAAAGGUA ACGGAGGCGC UCAAAGGUUC CCUCAGAAUG GUUGGAAAUC AUUCAUAGAG UGUAAAGGCA UAAGGGAGCU UGACUGCGAG ACCUACAAGU CGAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGCUACCCC GGGGAUAACA GGCUUAUCUC CCCCAAGAGU UCACAUCGAC GGGGAGGUUU GGCACCUCGA UGUCGGCUCA UCGCAUCCUG GGGCUGUAGU CGGUCCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGUAC GCGAGCUGGG UUCAGAACGU CGUGAGACAG UUCGGUCCCU AUCCGUCGUG GGCGUAGGAA AUUUGAGAGG AGCUGUCCUU AGUACGAGAG GACCGGGAUG GACAUACCUC UGGUGUACCA GUUGUCGUGC CAACGGCAUA GCUGGGUAGC UAUGUGUGGA CGGGAUAAGU GCUGAAAGCA UCUAAGCAUG AAGCCCCCCU CAAGAUGAGA UUUCCCAACU UCGGUUAUAA GAUCCCUCAA AGAUGAUGAG GUUAAUAGGU UCGAGGUGGA AGCAUGGUGA CAUGUGGAGC UGACGAAUAC UAAUCGAUCG AAGACUUAAU CAA
MassTheoretical: 946.696625 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #28: nucleic-acid, 5S rRNA

Nucleic-acidName: 5S rRNA5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGUCG AUGGUAGUCG AACUUACGUU CCGCUAGAGU AGAACGUUGC CAGGC
MassTheoretical: 36.974945 kDa
SourceSpecies: Staphylococcus aureus (bacteria)

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Component #29: ligand, 2-chloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2...

LigandName: 2-chloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.371791 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / Ph: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 49223
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF

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