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- PDB-7s1g: wild-type Escherichia coli stalled ribosome with antibiotic linezolid -

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Basic information

Entry
Database: PDB / ID: 7s1g
Titlewild-type Escherichia coli stalled ribosome with antibiotic linezolid
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • mRNAMessenger RNA
  • nascent peptide chain
  • tRNA(PHE)
KeywordsRIBOSOME/ANTIBIOTIC / Escherichia coli stalled ribosome / oxazolidinone / linezolid / RIBOSOME-ANTIBIOTIC complex
Function / homology
Function and homology information


positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly ...positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ribosome binding / large ribosomal subunit / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. ...Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L31 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / 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 L5, bacterial-type / Ribosomal protein L6, bacterial-type / 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 L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
Chem-ZLD / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS18 ...Chem-ZLD / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / 50S ribosomal protein L17 / 50S ribosomal protein L23 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L35 / 30S ribosomal protein S10 / 50S ribosomal protein L4 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 30S ribosomal protein S4 / 50S ribosomal protein L33 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 50S ribosomal protein L21 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L31 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 30S ribosomal protein S2 / 50S ribosomal protein L19 / 50S ribosomal protein L16 / 30S ribosomal protein S13 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L28
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsYoung, I.D. / Stojkovic, V. / Tsai, K. / Lee, D.J. / Fraser, J.S. / Galonic Fujimori, D.
Funding support11items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI137270
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI148120
Other governmentS10OD020054
Other governmentS10OD021741
Other governmentU24 GM129541
Other governmentU24 GM129539
Other governmentSimons Foundation (SF349247)
Other privateW.M. Keck Foundation Medical Research Grant
Other privateSangvhi-Agarwal Innovation Award
Other governmentNSF GRFP
Other privateUCSF Discovery Fellowship
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.
Authors: Kaitlyn Tsai / Vanja Stojković / D John Lee / Iris D Young / Teresa Szal / Dorota Klepacki / Nora Vázquez-Laslop / Alexander S Mankin / James S Fraser / Danica Galonić Fujimori /
Abstract: The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has ...The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Tristan Ian Croll /
Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density ...This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
#4: Journal: Protein Sci / Year: 2021
Title: UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Authors: Eric F Pettersen / Thomas D Goddard / Conrad C Huang / Elaine C Meng / Gregory S Couch / Tristan I Croll / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) ...UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.
History
DepositionSep 2, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn / struct_ref
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

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Assembly

Deposited unit
1: 30S ribosomal protein S19
2: 30S ribosomal protein S20
3: 30S ribosomal protein S21
4: mRNA
A: tRNA(PHE)
C: 16S rRNA
D: 30S ribosomal protein S2
E: 30S ribosomal protein S3
F: 30S ribosomal protein S4
G: 30S ribosomal protein S5
H: 30S ribosomal protein S6
I: 23S rRNA
J: 5S rRNA
K: 50S ribosomal protein L2
L: 50S ribosomal protein L3
M: 50S ribosomal protein L4
N: 50S ribosomal protein L5
O: 50S ribosomal protein L6
P: 50S ribosomal protein L9
Q: 50S ribosomal protein L31
R: 50S ribosomal protein L13
S: 50S ribosomal protein L14
T: 50S ribosomal protein L15
U: 50S ribosomal protein L16
V: 50S ribosomal protein L17
W: 50S ribosomal protein L18
X: 50S ribosomal protein L19
Y: 50S ribosomal protein L20
Z: 50S ribosomal protein L21
a: 50S ribosomal protein L22
b: 50S ribosomal protein L23
c: 50S ribosomal protein L24
d: 50S ribosomal protein L25
e: 50S ribosomal protein L27
f: 50S ribosomal protein L28
g: 50S ribosomal protein L29
h: 50S ribosomal protein L30
i: 50S ribosomal protein L32
j: 50S ribosomal protein L33
k: 50S ribosomal protein L34
l: 50S ribosomal protein L35
m: 50S ribosomal protein L36
n: 30S ribosomal protein S7
o: 30S ribosomal protein S8
p: 30S ribosomal protein S9
q: 30S ribosomal protein S10
r: 30S ribosomal protein S11
s: nascent peptide chain
t: 30S ribosomal protein S12
u: 30S ribosomal protein S13
v: 30S ribosomal protein S14
w: 30S ribosomal protein S15
x: 30S ribosomal protein S16
y: 30S ribosomal protein S17
z: 30S ribosomal protein S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,174,631254
Polymers2,169,39955
Non-polymers5,232199
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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30S ribosomal protein ... , 20 types, 20 molecules 123DEFGHnopqrtuvwxyz

#1: Protein 30S ribosomal protein S19 /


Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F9
#2: Protein 30S ribosomal protein S20 /


Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZAS2
#3: Protein 30S ribosomal protein S21 /


Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L2J1
#7: Protein 30S ribosomal protein S2 /


Mass: 26652.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZK99
#8: Protein 30S ribosomal protein S3 /


Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCS9
#9: Protein 30S ribosomal protein S4 /


Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9H7
#10: Protein 30S ribosomal protein S5 /


Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9H2
#11: Protein 30S ribosomal protein S6 / / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02358
#43: Protein 30S ribosomal protein S7 / / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02359
#44: Protein 30S ribosomal protein S8 /


Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G9
#45: Protein 30S ribosomal protein S9 /


Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZES9
#46: Protein 30S ribosomal protein S10 /


Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F4
#47: Protein 30S ribosomal protein S11 /


Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MCR3
#49: Protein 30S ribosomal protein S12 /


Mass: 13768.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZAN0
#50: Protein 30S ribosomal protein S13 /


Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: H4UQ02
#51: Protein 30S ribosomal protein S14 /


Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G8
#52: Protein 30S ribosomal protein S15 /


Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZEL4
#53: Protein 30S ribosomal protein S16 /


Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MIU7
#54: Protein 30S ribosomal protein S17 /


Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G4
#55: Protein 30S ribosomal protein S18 /


Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2KXL3

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RNA chain , 5 types, 5 molecules 4ACIJ

#4: RNA chain mRNA / Messenger RNA


Mass: 4737.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain tRNA(PHE)


Mass: 24509.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1841332652
#6: RNA chain 16S rRNA /


Mass: 499054.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1758835854
#12: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 941811.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#13: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1273279017

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50S ribosomal protein ... , 29 types, 29 molecules KLMNOPQRSTUVWXYZabcdefghijklm

#14: Protein 50S ribosomal protein L2 / / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60422
#15: Protein 50S ribosomal protein L3 / / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P60438
#16: Protein 50S ribosomal protein L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9F6
#17: Protein 50S ribosomal protein L5 /


Mass: 20333.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G7
#18: Protein 50S ribosomal protein L6 /


Mass: 18932.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9H0
#19: Protein 50S ribosomal protein L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZI15
#20: Protein 50S ribosomal protein L31 /


Mass: 7887.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZFP6
#21: Protein 50S ribosomal protein L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZET0
#22: Protein 50S ribosomal protein L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G5
#23: Protein 50S ribosomal protein L15 /


Mass: 15008.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#24: Protein 50S ribosomal protein L16 /


Mass: 15327.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: H4JDM7
#25: Protein 50S ribosomal protein L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D6I1Y5
#26: Protein 50S ribosomal protein L18 /


Mass: 12794.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9H1
#27: Protein 50S ribosomal protein L19 /


Mass: 13159.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZKU3
#28: Protein 50S ribosomal protein L20 /


Mass: 13528.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MAS6
#29: Protein 50S ribosomal protein L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZEN7
#30: Protein 50S ribosomal protein L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#31: Protein 50S ribosomal protein L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7X2Z9
#32: Protein 50S ribosomal protein L24 /


Mass: 11339.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G6
#33: Protein 50S ribosomal protein L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7XH79
#34: Protein 50S ribosomal protein L27 / / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A7L8
#35: Protein 50S ribosomal protein L28 /


Mass: 9027.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: S0YB49
#36: Protein 50S ribosomal protein L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9G3
#37: Protein 50S ribosomal protein L30 /


Mass: 6554.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9H3
#38: Protein 50S ribosomal protein L32 /


Mass: 6463.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7ZGG2
#39: Protein 50S ribosomal protein L33 /


Mass: 6388.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z9P0
#40: Protein/peptide 50S ribosomal protein L34 /


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: B7MGC4
#41: Protein 50S ribosomal protein L35 /


Mass: 7313.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: D7Z814
#42: Protein/peptide 50S ribosomal protein L36 /


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A0E2L017

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Protein/peptide , 1 types, 1 molecules s

#48: Protein/peptide nascent peptide chain


Mass: 643.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Non-polymers , 4 types, 241 molecules

#56: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 196 / Source method: obtained synthetically / Formula: Mg
#57: Chemical ChemComp-ZLD / N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide / Linezolid / Linezolid


Mass: 337.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20FN3O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#58: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#59: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: wild-type Escherichia coli stalled ribosome with antibiotic linezolid
Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL
Molecular weightValue: 2.154 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283.2 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 67.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3644

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cisTEMv1.0.0-betaCTF correction
7PHENIX1.19.2model fitting
8UCSF ChimeraX1.2.5 (2021-05-24)model fitting
9ISOLDE1.2.2model fitting
10Coot0.8.9.3-pre (revision-count 8011)model fitting
11PyMOLVersion 1.2r3premodel fitting
13cisTEMv1.0.0-betainitial Euler assignment
14cisTEMv1.0.0-betafinal Euler assignment
15cisTEMv1.0.0-betaclassification
16cisTEMv1.0.0-beta3D reconstruction
17PHENIX1.19.2model refinement
18ISOLDE1.2.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 332502
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176779 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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