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- PDB-6ddg: Structure of the 50S ribosomal subunit from Methicillin Resistant... -

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Entry
Database: PDB / ID: 6ddg
TitleStructure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-6
Components
  • (50S ribosomal protein ...) x 25
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
KeywordsRibosome/Antibiotic / antibiotic complex / linezolid / oxazolidinone / 50S / ribosome / Ribosome-Antibiotic complex
Function / homologyRibosomal protein L13 / Ribosomal protein L25, C-terminal / Ribosomal protein L20 / Ribosomal protein L36 / Ribosomal protein L30p/L7e / Ribosomal protein L3 / Ribosomal protein L23 / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / Ribosomal protein L22p/L17e ...Ribosomal protein L13 / Ribosomal protein L25, C-terminal / Ribosomal protein L20 / Ribosomal protein L36 / Ribosomal protein L30p/L7e / Ribosomal protein L3 / Ribosomal protein L23 / Ribosomal protein L16p/L10e / Ribosomal protein L14p/L23e / 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 L10e/L16 superfamily / Ribosomal protein L34 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L22/L17 superfamily / Ribosomal L18e/L15P superfamily / L21-like superfamily / 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 / KOW motif / Ribosomal protein L33 / Ribosomal protein L2, C-terminal / Ribosomal protein L22 signature. / Ribosomal protein L17 signature. / Ribosomal protein L24 signature. / Ribosomal protein L19 signature. / Ribosomal protein L20 signature. / Ribosomal protein L35 signature. / Ribosomal protein L27 signature. / Ribosomal protein L36 signature. / Ribosomal protein L34 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16 signature 1. / Ribosomal protein L33 signature. / Ribosomal protein L15 signature. / Ribosomal protein L3 signature. / Ribosomal protein L2 signature. / Ribosomal protein L14 signature. / Ribosomal protein L4/L1 family / 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 L19 / Ribosomal protein L17 / 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 L2, conserved site / Ribosomal protein L17 superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L21 / Ribosomal protein L20 / Ribosomal protein L15, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L18 / 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 L35, non-mitochondrial / Ribosomal protein L24/L26, conserved site / Ribosomal protein L35 / Ribosomal protein L27 / Ribosomal protein L28 / Ribosomal protein L15, conserved site / Ribosomal protein L22/L17 / Ribosomal protein L25, long-form / Ribosomal protein L3 / Ribosomal protein L36 / Ribosomal protein L17 / Ribosomal protein L34 / Ribosomal protein L14P / Ribosomal protein L16 / KOW / Ribosomal protein L33 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L19, conserved site / Ribosomal protein L34, conserved site
Function and homology information
Specimen sourceStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBelousoff, M.J. / Venugopal, H. / Bamert, R.S. / Lithgow, T.
Funding supportAustralia , 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)Program Grant 1092262Australia
CitationJournal: ChemMedChem / Year: 2019
Title: cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.
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 Report
SummaryFull reportAbout validation report
DateDeposition: May 10, 2018 / Release: Mar 20, 2019

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Structure visualization

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Assembly

Deposited unit
A: 50S ribosomal protein L19
B: 50S ribosomal protein L2
C: 50S ribosomal protein L20
D: 50S ribosomal protein L21
E: 50S ribosomal protein L22
F: 50S ribosomal protein L23
G: 50S ribosomal protein L24
H: 50S ribosomal protein L25
I: 50S ribosomal protein L27
J: 50S ribosomal protein L28
K: 50S ribosomal protein L29
L: 50S ribosomal protein L3
M: 50S ribosomal protein L30
N: 50S ribosomal protein L32
O: 50S ribosomal protein L33
P: 50S ribosomal protein L34
Q: 50S ribosomal protein L35
R: 50S ribosomal protein L36
S: 50S ribosomal protein L4
V: 50S ribosomal protein L13
W: 50S ribosomal protein L14
X: 50S ribosomal protein L15
Y: 50S ribosomal protein L16
Z: 50S ribosomal protein L17
a: 50S ribosomal protein L18
1: 23S rRNA
2: 5S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,306,29928
Polyers1,305,92827
Non-polymers3721
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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50S ribosomal protein ... , 25 types, 25 molecules ABCDEFGHIJKLMNOPQRSVWXYZa

#1: Protein/peptide 50S ribosomal protein L19 /


Mass: 13392.771 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UVB6
#2: Protein/peptide 50S ribosomal protein L2 /


Mass: 30087.984 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: B3VKN3
#3: Protein/peptide 50S ribosomal protein L20 /


Mass: 13720.295 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077VMP6
#4: Protein/peptide 50S ribosomal protein L21 /


Mass: 11354.081 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: D7URR3
#5: Protein/peptide 50S ribosomal protein L22 /


Mass: 12786.844 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UKF9
#6: Protein/peptide 50S ribosomal protein L23 /


Mass: 10625.398 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUB4
#7: Protein/peptide 50S ribosomal protein L24 /


Mass: 11561.504 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRD5
#8: Protein/peptide 50S ribosomal protein L25 / / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A133Q8Z9
#9: Protein/peptide 50S ribosomal protein L27 /


Mass: 9198.369 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077ULC5
#10: Protein/peptide 50S ribosomal protein L28 /


Mass: 6995.289 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077URJ8
#11: Protein/peptide 50S ribosomal protein L29 /


Mass: 8105.266 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077W1J5
#12: Protein/peptide 50S ribosomal protein L3 /


Mass: 23459.922 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8U3W0
#13: Protein/peptide 50S ribosomal protein L30 /


Mass: 6565.683 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8UVN7
#14: Protein/peptide 50S ribosomal protein L32 /


Mass: 6500.609 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UWR7
#15: Protein/peptide 50S ribosomal protein L33 /


Mass: 5885.783 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UXT4
#16: Protein/peptide 50S ribosomal protein L34 /


Mass: 5454.642 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: Q2YZB6
#17: Protein/peptide 50S ribosomal protein L35 /


Mass: 7593.188 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UL47
#18: Protein/peptide 50S ribosomal protein L36 /


Mass: 4318.422 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGV8
#19: Protein/peptide 50S ribosomal protein L4 /


Mass: 22523.752 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A166DK89
#20: Protein/peptide 50S ribosomal protein L13 /


Mass: 16359.427 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TUE6
#21: Protein/peptide 50S ribosomal protein L14 /


Mass: 13157.342 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UUA0
#22: Protein/peptide 50S ribosomal protein L15 /


Mass: 15628.890 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UGA7
#23: Protein/peptide 50S ribosomal protein L16 /


Mass: 16274.049 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077V4G0
#24: Protein/peptide 50S ribosomal protein L17 /


Mass: 13771.773 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: A0A077UG91
#25: Protein/peptide 50S ribosomal protein L18 /


Mass: 13124.093 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: W8TRE0

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RNA chain , 2 types, 2 molecules 12

#26: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 946696.625 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1269117575
#27: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source: (natural) Staphylococcus aureus (bacteria) / References: GenBank: 1333434557

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Non-polymers , 1 types, 1 molecules

#28: Chemical ChemComp-G6M / 2-chloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide / oxazolidinone antibiotic LZD-6


Mass: 371.791 Da / Num. of mol.: 1 / Formula: C16H19ClFN3O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 50S Ribosomal subunit from MRSA in complex with oxazolidinone LZD-5
Type: RIBOSOME
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Buffer solutionpH: 7.4
Buffer component

Buffer-ID: 1

IDConc. (mg/ml)Name
120 mMHEPES
240 mMPotassium Acetate
310 mMAmmonium Acetate
415 mMMagnesium Acetate
51 mMDTT
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49223 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.006987116
f_angle_d0.7518131214
f_chiral_restr0.043316901
f_plane_restr0.00526339
f_dihedral_angle_d16.430246068

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