EMDB-21887: Structure of the 50S subunit of the ribosome from Methicillin Res...

Basic information

• Entry: Database: EMDB / ID: EMD-21887
• Title: Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus aureus in complex with the antibiotic, tedizolid
• Map data: post-processed map

Sample

• Complex: 50S ribosomal subunitProkaryotic large ribosomal subunit
  • Protein or peptide: x 25 types
  • RNA: x 2 types
• Ligand: x 1 types

Function / homology

Function:

large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / cytoplasm

Domain/homology:

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, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L24 / Ribosomal protein L32p / 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 L15, conserved site / Ribosomal protein L2, conserved site / Ribosomal protein L2 signature. / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein L2, domain 3 / Ribosomal protein L14P, conserved site / Ribosomal protein L15 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal L29 protein / Ribosomal protein L24/L26, conserved site / Ribosomal protein L13, conserved site / Ribosomal protein L13 signature. / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal Proteins L2, C-terminal domain / Ribosomal protein L2, C-terminal / Ribosomal Proteins L2, C-terminal domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / Ribosomal protein L14 signature.

Component:

Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / 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 bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL21 / 50S ribosomal protein L4 / 50S ribosomal protein L29 / 50S ribosomal protein L25 / 50S ribosomal protein L22 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / 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 bL33B / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL30

• Biological species: Staphylococcus aureus (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 3.2 Å
• Authors: Belousoff MJ

Funding support

United States, 1 items

Organization	Grant number	Country
Department of Defense (DOD, United States)	W81XWH1910126	United States

• Citation: Journal: ACS Pharmacol Transl Sci / Year: 2020; Title: Characterization of the Core Ribosomal Binding Region for the Oxazolidone Family of Antibiotics Using Cryo-EM.; Authors: Alexander Wright / Kieran Deane-Alder / Edward Marschall / Rebecca Bamert / Hari Venugopal / Trevor Lithgow / David W Lupton / Matthew J Belousoff / ; Abstract: Linezolid and tedizolid are oxazolidinones with established clinical utility for the treatment of Gram-positive pathogens. Over time it has become apparent that even modest structural changes to the core phenyl oxazolidinone leads to drastic changes in biological activity. Consequently, the structure-activity relationship around the core oxazolidinone is constantly evolving, often reflected with new structural motifs present in nascent oxazolidinones. Herein we describe the use of cryo-electron microscopy to examine the differences in binding of several functionally different oxazolidinones in the hopes of enhanced understanding of their SAR. Tedizolid, radezolid, T145, and contezolid have been examined within the peptidyl transferase center (PTC) of the 50S ribosomal subunit from methicillin resistant . The ribosome-antibiotic complexes were resolved to a resolution of around 3 Å enabling unambiguous assignment of how each antibiotic interacts with the PTC.

History

Deposition	Apr 30, 2020	-
Header (metadata) release	Jun 3, 2020	-
Map release	Jun 3, 2020	-
Update	Dec 16, 2020	-
Current status	Dec 16, 2020	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_21887.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: post-processed map
• Voxel size: X=Y=Z: 1.14 Å

Density

Contour Level	By AUTHOR: 0.02 / Movie #1: 0.05
Minimum - Maximum	-0.24728741 - 0.43174118
Average (Standard dev.)	0.00032124578 (±0.010915102)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 360 360 360 Spacing 360 360 360
Cell	A=B=C: 410.4 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.14	1.14	1.14
M x/y/z	360	360	360
origin x/y/z	0.000	0.000	0.000
length x/y/z	410.400	410.400	410.400
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	360	360	360
D min/max/mean	-0.247	0.432	0.000

Supplemental data

Additional map: Unsharpened map

• File: emd_21887_additional.map
• Annotation: Unsharpened map

Half map: #1

• File: emd_21887_half_map_1.map

Half map: #2

• File: emd_21887_half_map_2.map

Sample components

Entire : 50S ribosomal subunit

• Entire: Name: 50S ribosomal subunitProkaryotic large ribosomal subunit

Components

• Complex: 50S ribosomal subunitProkaryotic large ribosomal subunit
  • Protein or peptide: 50S ribosomal protein L19
  • Protein or peptide: 50S ribosomal protein L2
  • Protein or peptide: 50S ribosomal protein L20
  • Protein or peptide: 50S ribosomal protein L21
  • Protein or peptide: uL22
  • Protein or peptide: 50S ribosomal protein L23
  • Protein or peptide: 50S ribosomal protein L24
  • Protein or peptide: uL25
  • Protein or peptide: 50S ribosomal protein L28
  • Protein or peptide: 50S ribosomal protein L29
  • Protein or peptide: 50S ribosomal protein L3
  • Protein or peptide: 50S ribosomal protein L30
  • 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
  • Protein or peptide: 50S ribosomal protein L4
  • 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
  • RNA: 23S rRNA23S ribosomal RNA
  • RNA: 5S rRNA5S ribosomal RNA
  • Protein or peptide: 50S ribosomal protein L27
• Ligand: Tedizolid

Supramolecule #1: 50S ribosomal subunit

• Supramolecule: Name: 50S ribosomal subunit / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#27
• Source (natural): Organism: Staphylococcus aureus (bacteria)

Macromolecule #1: 50S ribosomal protein L19

• Macromolecule: Name: 50S ribosomal protein L19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.392771 KDa

Sequence

String:

MTNHKLIEAV TKSQLRTDLP SFRPGDTLRV HVRIIEGTRE RIQVFEGVVI KRRGGGVSET FTVRKISSGV GVERTFPLHT PKIEKIEVK RRGKVRRAKL YYLRSLRGKA ARIQEIR

Macromolecule #2: 50S ribosomal protein L2

• Macromolecule: Name: 50S ribosomal protein L2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 30.217164 KDa

Sequence

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

Macromolecule #3: 50S ribosomal protein L20

• Macromolecule: Name: 50S ribosomal protein L20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.720295 KDa

Sequence

String:

MPRVKGGTVT RARRKKTIKL AKGYFGSKHT LYKVAKQQVM KSGQYAFRDR RQRKRDFRKL WITRINAAAR QHEMSYSRLM NGLKKAGID INRKMLSEIA ISDEKAFAQL VTKAKDALK

Macromolecule #4: 50S ribosomal protein L21

• Macromolecule: Name: 50S ribosomal protein L21 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 11.700483 KDa

Sequence

String:

MQSMFAIIET GGKQIKVEEG QEIFVEKLDV NEGDTFTFDK VLFVGGDSVK VGAPTVEGAT VTATVNKQGR GKKITVFTYK RRKNSKRKK GHRQPYTKLT IDKINA

Macromolecule #5: uL22

• Macromolecule: Name: uL22 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 12.871947 KDa

Sequence

String:

MEAKAVARTI RIAPRKVRLV LDLIRGKNAA EAIAILKLTN KASSPVIEKV LMSALANAEH NYDMNTDELV VKEAYANEGP TLKRFRPRA QGRASAINKR TSHITIVVSD AKEEAKEA

Macromolecule #6: 50S ribosomal protein L23

• Macromolecule: Name: 50S ribosomal protein L23 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 10.627328 KDa

Sequence

String:

MEARDILKRP VITEKSSEAM AEDKYTFDVD TRVNKTQVKM AVEEIFNVKV ASVNIMNYKP KKKRMGRYQG YTNKRRKAIV TLKEGSDDL FN

Macromolecule #7: 50S ribosomal protein L24

• Macromolecule: Name: 50S ribosomal protein L24 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 11.59153 KDa

Sequence

String:

MHIKKGDNVK VIAGKDKGKE GKVIATLPKK DRVVVEGVNI MKKHQKPTQL NPESGILETE AAIHVSNVQL LDPKTNEPTR VGYKFVDGK KVRIAKKSGE EIKSNN

Macromolecule #8: uL25

• Macromolecule: Name: uL25 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 12.063077 KDa

Sequence

String:

MASLKSIIRQ GKQTRSDLKQ LRKSGKVPAV VYGYGTKNVS VKVDEVEFIK VIREVGRNGV IELGVGSKTI KVMVADYQFD PLKNQITHI DFLAINMSED VLLKYQFN

Macromolecule #9: 50S ribosomal protein L28

• Macromolecule: Name: 50S ribosomal protein L28 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 6.967235 KDa

Sequence

String:

MGKQCFVTGR KASTGNRRSH ALNSTKRRWN ANLQKVRILV DGKPKKVWVS ARALKSGKVT RA

Macromolecule #10: 50S ribosomal protein L29

• Macromolecule: Name: 50S ribosomal protein L29 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 8.49182 KDa

Sequence

String:

MKKKKAKEIR NLTTSEIEEQ IKSSKEELFN LRFQLATGQL EETARIRTVR KTIARLKTVA REREIEQSKA NQ

Macromolecule #11: 50S ribosomal protein L3

• Macromolecule: Name: 50S ribosomal protein L3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 23.459922 KDa

Sequence

String:

MTKGILGRKI GMTQVFGENG ELIPVTVVEA KENVVLQKKT VEVDGYNAIQ VGFEDKKAYK KDAKSNKYAN KPAEGHAKKA DAAPKRFIR EFRNVDVDAY EVGQEVSVDT FVAGDVIDVT GVSKGKGFQG AIKRHGQSRG PMSHGSHFHR APGSVGMASD A SRVFKGQK MPGRMGGNTV TVQNLEVVQV DTENKVILVK GNVPGPKKGL VEIRTSIKK

Macromolecule #12: 50S ribosomal protein L30

• Macromolecule: Name: 50S ribosomal protein L30 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 6.434487 KDa

Sequence

String:

AKLQITLTRS VIGRPETQRK TVEALGLKKT NSSVVVEDNP AIRGQINKVK HLVTVEEK

Macromolecule #13: 50S ribosomal protein L32

• Macromolecule: Name: 50S ribosomal protein L32 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 6.472556 KDa

Sequence

String:

MAVPKRRTSK TRKNKRRTHF KISVPGMTEC PNCGEYKLSH RVCKNCGSYN GEEAAAK

Macromolecule #14: 50S ribosomal protein L33

• Macromolecule: Name: 50S ribosomal protein L33 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 5.885783 KDa

Sequence

String:

MRVNVTLACT ECGDRNYITT KNKRNNPERV EMKKFCSREN KQTLHRETK

Macromolecule #15: 50S ribosomal protein L34

• Macromolecule: Name: 50S ribosomal protein L34 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 6.0644 KDa

Sequence

String:

MEVFCMVKRT YQPNKRKHSK VHGFRKRMST KNGRKVLARR RRKGRKVLSA

Macromolecule #16: 50S ribosomal protein L35

• Macromolecule: Name: 50S ribosomal protein L35 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 7.593188 KDa

Sequence

String:

MPKMKTHRGA AKRVKRTASG QLKRSRAFTS HLFANKSTKQ KRQLRKARLV SKSDMKRVKQ LLAYK

Macromolecule #17: 50S ribosomal protein L36

• Macromolecule: Name: 50S ribosomal protein L36 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 4.318422 KDa

Sequence

String:

MKVRPSVKPI CEKCKVIKRK GKVMVICENP KHKQRQG

Macromolecule #18: 50S ribosomal protein L4

• Macromolecule: Name: 50S ribosomal protein L4 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 22.523752 KDa

Sequence

String:

MANYDVLKLD GTKSGSIELS DAVFGIEPNN SVLFEAINLQ RASLRQGTHA VKNRSAVSGG GRKPWKQKGT GRARQGTIRA PQWRGGGIV FGPTPRSYAY KMPKKMRRLA LRSALSFKVQ ENGLTVVDAF NFEAPKTKEF KNVLSTLEQP KKVLVVTENE D VNVELSAR NIPGVQVTTA QGLNVLDITN ADSLVITEAA AKKVEEVLG

Macromolecule #19: 50S ribosomal protein L13

• Macromolecule: Name: 50S ribosomal protein L13 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 16.359427 KDa

Sequence

String:

MRQTFMANES NIERKWYVID AEGQTLGRLS SEVASILRGK NKVTYTPHVD TGDYVIVINA SKIEFTGNKE TDKVYYRHSN HPGGIKSIT AGELRRTNPE RLIENSIKGM LPSTRLGEKQ GKKLFVYGGA EHPHAAQQPE NYELRG

Macromolecule #20: 50S ribosomal protein L14

• Macromolecule: Name: 50S ribosomal protein L14 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.157342 KDa

Sequence

String:

MIQQETRLKV ADNSGAREVL TIKVLGGSGR KTANIGDVIV CTVKNATPGG VVKKGDVVKA VIVRTKSGVR RNDGSYIKFD ENACVIIRD DKGPRGTRIF GPVARELREG NFMKIVSLAP EVL

Macromolecule #21: 50S ribosomal protein L15

• Macromolecule: Name: 50S ribosomal protein L15 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 15.62889 KDa

Sequence

String:

MKLHELKPAE GSRKERNRVG RGVATGNGKT SGRGHKGQKA RSGGGVRPGF EGGQLPLFRR LPKRGFTNIN RKEYAIVNLD QLNKFEDGT EVTPALLVES GVVKNEKSGI KILGNGSLDK KLTVKAHKFS ASAAEAIDAK GGAHEVI

Macromolecule #22: 50S ribosomal protein L16

• Macromolecule: Name: 50S ribosomal protein L16 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 16.274049 KDa

Sequence

String:

MLLPKRVKYR RQHRPKTTGR SKGGNYVTFG EFGLQATTTS WITSRQIESA RIAMTRYMKR GGKVWIKIFP HTPYTKKPLE VRMGAGKGA VEGWIAVVKP GRILFEVAGV SEEVAREALR LASHKLPVKT KFVKREELGG ETNES

Macromolecule #23: 50S ribosomal protein L17

• Macromolecule: Name: 50S ribosomal protein L17 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.771773 KDa

Sequence

String:

MGYRKLGRTS DQRKAMLRDL ATSLIISERI ETTEARAKEV RSVVEKLITL GKKGDLASRR NAAKTLRNVE ILNEDETTQT ALQKLFGEI AERYTERQGG YTRILKQGPR RGDGAESVII ELV

Macromolecule #24: 50S ribosomal protein L18

• Macromolecule: Name: 50S ribosomal protein L18 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 13.124093 KDa

Sequence

String:

MISKIDKNKV RLKRHARVRT NLSGTAEKPR LNVYRSNKHI YAQIIDDNKG VTLAQASSKD SDIATTATKV ELATKVGEAI AKKAADKGI KEIVFDRGGY LYHGRVKALA EAARESGLEF

Macromolecule #27: 50S ribosomal protein L27

• Macromolecule: Name: 50S ribosomal protein L27 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 9.198369 KDa

Sequence

String:

ASKKGVSSTK NGRDSESKRL GAKRADGQFV TGGSILYRQR GTKIYPGENV GRGGDDTLFA KIDGVVKFER KGRDKKQVSV YAVAE

Macromolecule #25: 23S rRNA

• Macromolecule: Name: 23S rRNA / type: rna / ID: 25 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 946.680625 KDa

Sequence

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 CUCUAUACGG 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 UGAAAAGUG AGCGGAUGAA CUGAGGGUAG CGGAGAAAUU CCAAUCGAAC CUGGAGAUAG CUGGUUCUCU CCGAAAUAGC UUUAGGGCUA GCCUCAAGU GAUGAUUAUU GGAGGUAGAG CACUGUUUGG ACGAGGGGCC CCUCUCGGGU UACCGAAUUC AGACAAACUC C GAAUGCCA AUUAAUUUAA CUUGGGAGUC AGAACAUGGG UGAUAAGGUC CGUGUUCGAA AGGGAAACAG CCCAGACCAC CA GCUAAGG UCCCAAAAUA UAUGUUAAGU GGAAAAGGAU GUGGCGUUGC CCAGACAACU AGGAUGUUGG CUUAGAAGCA GCC AUCAUU UAAAGAGUGC GUAAUAGCUC ACUAGUCGAG UGACACUGCG CCGAAAAUGU ACCGGGGCUA AACAUAUUAC CGAA GCUGU GGAUUGUCCU UUGGACAAUG GUAGGAGAGC GUUCUAAGGG CGUUGAAGCA UGAUCGUAAG GACAUGUGGA GCGCU UAGA AGUGAGAAUG CCGGUGUGAG UAGCGAAAGA CGGGUGAGAA UCCCGUCCAC CGAUUGACUA AGGUUUCCAG AGGAAG GCU CGUCCGCUCU GGGUUAGUCG GGUCCUAAGC UGAGGCCGAC AGGCGUAGGC GAUGGAUAAC AGGUUGAUAU UCCUGUA CC ACCUAUAAUC GUUUUAAUCG AUGGGGGGAC GCAGUAGGAU AGGCGAAGCG UGCGAUUGGA UUGCACGUCU AAGCAGUA A GGCUGAGUAU UAGGCAAAUC CGGUACUCGU UAAGGCUGAG CUGUGAUGGG GAGAAGACAU UGUGUCUUCG AGUCGUUGA UUUCACACUG CCGAGAAAAG CCUCUAGAUA GAAAAUAGGU GCCCGUACCG CAAACCGACA CAGGUAGUCA AGAUGAGAAU UCUAAGGUG AGCGAGCGAA CUCUCGUUAA GGAACUCGGC AAAAUGACCC CGUAACUUCG GGAGAAGGGG UGCUCUUUAG G GUUAACGC CCAGAAGAGC CGCAGUGAAU AGGCCCAAGC GACUGUUUAU CAAAAACACA GGUCUCUGCU AAACCGUAAG GU GAUGUAU AGGGGCUGAC GCCUGCCCAG UGCUGGAAGG UUAAGAGGAG UGGUUAGCUU CUGCGAAGCU ACGAAUCGAA GCC CCAGUA AACGGCGGCC GUAACUAUAA CGGUCCUAAG GUAGCGAAAU UCCUUGUCGG GUAAGUUCCG ACCCGCACGA AAGG CGUAA CGAUUUGGGC ACUGUCUCAA CGAGAGACUC GGUGAAAUCA UAGUACCUGU GAAGAUGCAG GUUACCCGCG ACAGG ACGG AAAGACCCCG UGGAGCUUUA CUGUAGCCUG AUAUUGAAAU UCGGCACAGC UUGUACAGGA UAGGUAGGAG CCUUUG AAA CGUGAGCGCU AGCUUACGUG GAGGCGCUGG UGGGAUACUA CCCUAGCUGU GUUGGCUUUC UAACCCGCAC CACUUAU CG UGGUGGGAGA CAGUGUCAGG CGGGCAGUUU GACUGGGGCG GUCGCCUCCU AAAAGGUAAC GGAGGCGCUC AAAGGUUC C CUCAGAAUGG UUGGAAAUCA UUCAUAGAGU GUAAAGGCAU AAGGGAGCUU GACUGCGAGA CCUACAAGUC GAGCAGGGU CGAAAGACGG ACUUAGUGAU CCGGUGGUUC CGCAUGGAAG GGCCAUCGCU CAACGGAUAA AAGCUACCCC GGGGAUAACA GGCUUAUCU CCCCCAAGAG UUCACAUCGA CGGGGAGGUU UGGCACCUCG AUGUCGGCUC AUCGCAUCCU GGGGCUGUAG U CGGUCCCA AGGGUUGGGC UGUUCGCCCA UUAAAGCGGU ACGCGAGCUG GGUUCAGAAC GUCGUGAGAC AGUUCGGUCC CU AUCCGUC GUGGGCGUAG GAAAUUUGAG AGGAGCUGUC CUUAGUACGA GAGGACCGGG AUGGACAUAC CUCUGGUGUA CCA GUUGUC GUGCCAACGG CAUAGCUGGG UAGCUAUGUG UGGACGGGAU AAGUGCUGAA AGCAUCUAAG CAUGAAGCCC CCCU CAAGA UGAGAUUUCC CAACUUCGGU UAUAAGAUCC CUCAAAGAUG AUGAGGUUAA UAGGUUCGAG GUGGAAGCAU GGUGA CAUG UGGAGCUGAC GAAUACUAAU CGAUCGAAGA CUUAAUCAA

Macromolecule #26: 5S rRNA

• Macromolecule: Name: 5S rRNA / type: rna / ID: 26 / Number of copies: 1
• Source (natural): Organism: Staphylococcus aureus (bacteria)
• Molecular weight: Theoretical: 36.957961 KDa

Sequence

String:

UCUGGUGACU AUAGCAAGGA GGUCACACCU GUUCCCAUGC CGAACACAGA AGUUAAGCUC CUUAGCGACG AUGGUAGUCC AACUUACGU UCCGCUAGAG UAGAACGUUC CAGGGC

Macromolecule #28: Tedizolid

• Macromolecule: Name: Tedizolid / type: ligand / ID: 28 / Number of copies: 1 / Formula: U7V
• Molecular weight: Theoretical: 370.338 Da

Chemical component information

ChemComp-U7V:
Tedizolid / antibiotic*YM / Tedizolid

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 0.3 mg/mL
• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS GLACIOS
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Ų

Image processing

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD
• Final angle assignment: Type: MAXIMUM LIKELIHOOD
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140000