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- PDB-7ood: Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol... -

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Basic information

Entry
Database: PDB / ID: 7ood
TitleMycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol-treated cells
Components
  • (50S ribosomal protein ...) x 29
  • 23S ribosomal RNA
  • 5S ribosomal RNA
KeywordsRIBOSOME / In-cell cryo-electron tomography chloramphenicol-treated sub-tomogram analysis
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding ...large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / cytoplasm
Similarity search - Function
Ribosomal protein L9, C-terminal domain / Ribosomal Protein L9; domain 2 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Ribosomal protein L10, eubacterial, conserved site ...Ribosomal protein L9, C-terminal domain / Ribosomal Protein L9; domain 2 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L6 / Ribosomal protein L22/L17 / Ribosomal Protein L22; Chain A / Outer Surface Protein A; domain 3 / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / 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 protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L36 signature. / Ribosomal protein L32p, bacterial type / Ribosomal protein L28/L24 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / : / Ribosomal protein L5, bacterial-type / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L16 / Ribosomal protein L28/L24 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / : / L28p-like / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L20 / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal
Similarity search - Domain/homology
CHLORAMPHENICOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 ...CHLORAMPHENICOL / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 3.4 Å
AuthorsXue, L. / Lenz, S. / Rappsilber, J. / Mahamid, J.
Funding support Germany, United Kingdom, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)426290502 Germany
Wellcome Trust103139 United Kingdom
Wellcome Trust203149 United Kingdom
Citation
Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#1: Journal: Nature / Year: 2022
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell.
Authors: Liang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
Abstract: Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
#2: Journal: Biorxiv / Year: 2021
Title: Visualizing translation dynamics at atomic detail inside a bacterial cell
Authors: Xue, L. / Lenz, S. / Zimmermann-Kogadeeva, M. / Tegunov, D. / Cramer, P. / Bork, P. / Rappsilber, J. / Mahamid, J.
History
DepositionMay 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: 23S ribosomal RNA
4: 5S ribosomal RNA
w: 50S ribosomal protein L29
a: 50S ribosomal protein L2
c: 50S ribosomal protein L4
e: 50S ribosomal protein L6
k: 50S ribosomal protein L15
i: 50S ribosomal protein L13
m: 50S ribosomal protein L17
q: 50S ribosomal protein L21
u: 50S ribosomal protein L27
y: 50S ribosomal protein L32
0: 50S ribosomal protein L34
2: 50S ribosomal protein L36
1: 50S ribosomal protein L35
o: 50S ribosomal protein L19
s: 50S ribosomal protein L23
v: 50S ribosomal protein L28
x: 50S ribosomal protein L31
z: 50S ribosomal protein L33 1
d: 50S ribosomal protein L5
b: 50S ribosomal protein L3
l: 50S ribosomal protein L16
p: 50S ribosomal protein L20
j: 50S ribosomal protein L14
n: 50S ribosomal protein L18
t: 50S ribosomal protein L24
r: 50S ribosomal protein L22
f: 50S ribosomal protein L9
h: 50S ribosomal protein L11
g: 50S ribosomal protein L10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,413,16161
Polymers1,411,99431
Non-polymers1,16630
Water00
1


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

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Components

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RNA chain , 2 types, 2 molecules 34

#1: RNA chain 23S ribosomal RNA


Mass: 940911.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129
#2: RNA chain 5S ribosomal RNA


Mass: 34796.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129

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50S ribosomal protein ... , 29 types, 29 molecules wacekimquy021osvxzdblpjntrfhg

#3: Protein 50S ribosomal protein L29


Mass: 13003.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50310
#4: Protein 50S ribosomal protein L2


Mass: 31966.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75577
#5: Protein 50S ribosomal protein L4


Mass: 23632.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75579
#6: Protein 50S ribosomal protein L6


Mass: 20624.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q50303
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50303
#7: Protein 50S ribosomal protein L15


Mass: 16768.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q50300
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50300
#8: Protein 50S ribosomal protein L13


Mass: 16821.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75178
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75178
#9: Protein 50S ribosomal protein L17


Mass: 14270.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q59547
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q59547
#10: Protein 50S ribosomal protein L21


Mass: 11664.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P78026
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P78026
#11: Protein 50S ribosomal protein L27


Mass: 11527.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75458
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75458
#12: Protein 50S ribosomal protein L32


Mass: 6641.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75238
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75238
#13: Protein/peptide 50S ribosomal protein L34


Mass: 5616.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P78006
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P78006
#14: Protein/peptide 50S ribosomal protein L36


Mass: 4400.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P52864
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P52864
#15: Protein 50S ribosomal protein L35


Mass: 6793.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75447
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75447
#16: Protein 50S ribosomal protein L19


Mass: 13870.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75133
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75133
#17: Protein 50S ribosomal protein L23


Mass: 25892.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75578
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75578
#18: Protein 50S ribosomal protein L28


Mass: 7549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75171
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75171
#19: Protein 50S ribosomal protein L31


Mass: 10980.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P78020
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P78020
#20: Protein 50S ribosomal protein L33 1


Mass: 6298.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P78015
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P78015
#21: Protein 50S ribosomal protein L5


Mass: 20270.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q50306
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50306
#22: Protein 50S ribosomal protein L3


Mass: 31298.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75580
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75580
#23: Protein 50S ribosomal protein L16


Mass: 15646.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P41204
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P41204
#24: Protein 50S ribosomal protein L20


Mass: 14742.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P78023
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P78023
#25: Protein 50S ribosomal protein L14


Mass: 13478.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P41204
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50308
#26: Protein 50S ribosomal protein L18


Mass: 13073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q50302
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50302
#27: Protein 50S ribosomal protein L24


Mass: 12461.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Q50307
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: Q50307
#28: Protein 50S ribosomal protein L22


Mass: 17355.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75575
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75575
#29: Protein 50S ribosomal protein L9


Mass: 17185.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75540
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75540
#30: Protein 50S ribosomal protein L11


Mass: 14803.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75550
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75550
#31: Protein 50S ribosomal protein L10


Mass: 17645.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: P75240
Source: (natural) Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Strain: ATCC 29342 / M129 / References: UniProt: P75240

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Non-polymers , 4 types, 30 molecules

#32: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#33: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#34: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#35: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: cryo-electron tomograms of chloramphenicol-treated Mycoplasma pneumoniae cells
Type: RIBOSOME
Details: ribosome sub-tomograms extracted in silico from cellular tomograms, focused refinement on 50S
Entity ID: #1-#31 / Source: NATURAL
Source (natural)Organism: Mycoplasma pneumoniae (strain ATCC 29342 / M129) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Mycoplasma pneumoniae M129 cells grown on gold Quantifoil grids at 37 degrees Celsius before plunge freezing.
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: ack-side blotting for 2-3 second before plunging using a manual plunger without an environmental chamber

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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 FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3750 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 3.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.1_3865+SVNrefinement
PHENIX1.18.1_3865+SVNrefinement
EM software
IDNameVersionCategoryDetails
9Coot0.9model refinement
10PHENIX1.18model refinementphenix real-space refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17890
Details: Map generated by focused refinement on the 50S subunit in M
Symmetry type: POINT
EM volume selectionNum. of tomograms: 65 / Num. of volumes extracted: 17890
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
13J9W

3j9w

3J9W1
21DIV

1div

f1DIV2
31ZAV

1zav

g1ZAV3
44YBB

4ybb

34YBB4
54YBB

4ybb

44YBB4
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 83.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.010597517
ELECTRON MICROSCOPYf_angle_d1.3495146523
ELECTRON MICROSCOPYf_chiral_restr0.105818948
ELECTRON MICROSCOPYf_plane_restr0.00927448
ELECTRON MICROSCOPYf_dihedral_angle_d18.57845317

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