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- PDB-7pas: 70S ribosome with P/E-site tRNA in Mycoplasma pneumoniae cells -

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Basic information

Entry
Database: PDB / ID: 7pas
Title70S ribosome with P/E-site tRNA in Mycoplasma pneumoniae cells
Components
  • (30S ribosomal protein ...) x 20
  • (50S ribosomal protein ...) x 29
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • tRNA-Phe
KeywordsTRANSLATION / In-cell cryo-electron tomography / sub-tomogram analysis / ribosome / translation intermediate state
Function / homology
Function and homology information


large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding ...large ribosomal subunit / transferase activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / 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 / RNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 / Ribosomal protein L31 signature. ...Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / : / Ribosomal protein S14, type Z / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein S21 / 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, conserved site / Ribosomal protein L16 signature 2. / 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 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 L17 signature. / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / 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 S14/S29 / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S13, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L36 / Ribosomal protein S11, bacterial-type / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S4, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L20 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L14P, bacterial-type / Ribosomal protein S2, bacteria/mitochondria/plastid / 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 protein S18, conserved site
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein uL16 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS20 / 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 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL3 / Small ribosomal subunit protein uS10 / 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 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesMycoplasma pneumoniae M129 (bacteria)
Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 16 Å
AuthorsXue, L. / Lenz, S. / Rappsilber, J. / Mahamid, J.
Funding support Germany, United Kingdom, 4items
OrganizationGrant numberCountry
European Research Council (ERC)760067 Germany
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: 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
DepositionJul 30, 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 1.3Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / 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 / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 50S ribosomal protein L34
1: 50S ribosomal protein L35
2: 50S ribosomal protein L36
A: 30S ribosomal protein S2
B: 30S ribosomal protein S3
C: 30S ribosomal protein S4
D: 30S ribosomal protein S5
E: 30S ribosomal protein S6
F: 30S ribosomal protein S7
G: 30S ribosomal protein S8
H: 30S ribosomal protein S9
I: 30S ribosomal protein S10
J: 30S ribosomal protein S11
K: 30S ribosomal protein S12
L: 30S ribosomal protein S13
M: 30S ribosomal protein S14 type Z
N: 30S ribosomal protein S15
O: 30S ribosomal protein S16
P: 30S ribosomal protein S17
Q: 30S ribosomal protein S18
R: 30S ribosomal protein S19
S: 30S ribosomal protein S20
T: 30S ribosomal protein S21
a: 50S ribosomal protein L2
b: 50S ribosomal protein L3
c: 50S ribosomal protein L4
d: 50S ribosomal protein L5
e: 50S ribosomal protein L6
f: 50S ribosomal protein L9
g: 50S ribosomal protein L10
h: 50S ribosomal protein L11
i: 50S ribosomal protein L13
j: 50S ribosomal protein L14
k: 50S ribosomal protein L15
l: 50S ribosomal protein L16
m: 50S ribosomal protein L17
n: 50S ribosomal protein L18
o: 50S ribosomal protein L19
p: 50S ribosomal protein L20
q: 50S ribosomal protein L21
r: 50S ribosomal protein L22
s: 50S ribosomal protein L23
t: 50S ribosomal protein L24
u: 50S ribosomal protein L27
v: 50S ribosomal protein L28
w: 50S ribosomal protein L29
x: 50S ribosomal protein L31
y: 50S ribosomal protein L32
z: 50S ribosomal protein L33 1
3: 23S ribosomal RNA
4: 5S ribosomal RNA
5: 16S ribosomal RNA
8: tRNA-Phe


Theoretical massNumber of molelcules
Total (without water)2,246,47553
Polymers2,246,47553
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area327770 Å2
ΔGint-2517 kcal/mol
Surface area594300 Å2

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Components

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50S ribosomal protein ... , 29 types, 29 molecules 012abcdefghijklmnopqrstuvwxyz

#1: Protein/peptide 50S ribosomal protein L34


Mass: 5616.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P78006
#2: Protein 50S ribosomal protein L35


Mass: 6793.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75447
#3: Protein/peptide 50S ribosomal protein L36


Mass: 4400.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P52864
#24: Protein 50S ribosomal protein L2


Mass: 31966.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75577
#25: Protein 50S ribosomal protein L3


Mass: 31298.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75580
#26: Protein 50S ribosomal protein L4


Mass: 23632.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75579
#27: Protein 50S ribosomal protein L5


Mass: 20270.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50306
#28: Protein 50S ribosomal protein L6


Mass: 20624.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50303
#29: Protein 50S ribosomal protein L9


Mass: 17185.037 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: P75540
#30: Protein 50S ribosomal protein L10


Mass: 17645.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75240
#31: Protein 50S ribosomal protein L11


Mass: 14803.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75550
#32: Protein 50S ribosomal protein L13


Mass: 16821.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75178
#33: Protein 50S ribosomal protein L14


Mass: 13478.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50308
#34: Protein 50S ribosomal protein L15


Mass: 16768.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50300
#35: Protein 50S ribosomal protein L16


Mass: 15646.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P41204
#36: Protein 50S ribosomal protein L17


Mass: 14270.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q59547
#37: Protein 50S ribosomal protein L18


Mass: 13073.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50302
#38: Protein 50S ribosomal protein L19


Mass: 13870.327 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: P75133
#39: Protein 50S ribosomal protein L20


Mass: 14742.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P78023
#40: Protein 50S ribosomal protein L21


Mass: 11664.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P78026
#41: Protein 50S ribosomal protein L22


Mass: 17355.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75575
#42: Protein 50S ribosomal protein L23


Mass: 25892.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75578
#43: Protein 50S ribosomal protein L24


Mass: 12461.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50307
#44: Protein 50S ribosomal protein L27


Mass: 11527.338 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75458
#45: Protein 50S ribosomal protein L28


Mass: 7549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75171
#46: Protein 50S ribosomal protein L29


Mass: 13003.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50310
#47: Protein 50S ribosomal protein L31


Mass: 10980.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P78020
#48: Protein 50S ribosomal protein L32


Mass: 6641.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75238
#49: Protein 50S ribosomal protein L33 1


Mass: 6298.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P78015

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30S ribosomal protein ... , 20 types, 20 molecules ABCDEFGHIJKLMNOPQRST

#4: Protein 30S ribosomal protein S2


Mass: 33468.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75560
#5: Protein 30S ribosomal protein S3


Mass: 30657.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P41205
#6: Protein 30S ribosomal protein S4


Mass: 23817.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P46775
#7: Protein 30S ribosomal protein S5


Mass: 24138.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50301
#8: Protein 30S ribosomal protein S6


Mass: 25430.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75543
#9: Protein 30S ribosomal protein S7


Mass: 17897.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75545
#10: Protein 30S ribosomal protein S8


Mass: 15903.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50304
#11: Protein 30S ribosomal protein S9


Mass: 15149.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75179
#12: Protein 30S ribosomal protein S10


Mass: 12226.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75581
#13: Protein 30S ribosomal protein S11


Mass: 12709.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50296
#14: Protein 30S ribosomal protein S12


Mass: 15666.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75546
#15: Protein 30S ribosomal protein S13


Mass: 14209.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50297
#16: Protein 30S ribosomal protein S14 type Z


Mass: 6901.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50305
#17: Protein 30S ribosomal protein S15


Mass: 9921.687 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75173
#18: Protein 30S ribosomal protein S16


Mass: 10806.921 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: A0A0H3DLS7
#19: Protein 30S ribosomal protein S17


Mass: 9859.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: Q50309
#20: Protein 30S ribosomal protein S18


Mass: 12411.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75541
#21: Protein 30S ribosomal protein S19


Mass: 10057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75576
#22: Protein 30S ribosomal protein S20


Mass: 9993.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P75237
#23: Protein 30S ribosomal protein S21


Mass: 7539.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria) / References: UniProt: P57079

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RNA chain , 4 types, 4 molecules 3458

#50: RNA chain 23S ribosomal RNA


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


Mass: 34796.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria)
#52: RNA chain 16S ribosomal RNA


Mass: 491243.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria)
#53: RNA chain tRNA-Phe


Mass: 24470.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasma pneumoniae M129 (bacteria)

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Details

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 untreated Mycoplasma pneumoniae cells
Type: CELL
Details: Ribosome sub-tomograms extracted in silico from tomograms of intact cell, refinement with a 70S mask
Entity ID: all / Source: NATURAL
Source (natural)Organism: Mycoplasma pneumoniae 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 Celsius before plunge freezing.
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE
Details: back-side blotting for 2-3 seconds 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

EM software
IDNameVersionCategoryDetails
2Warp3.0.7 beta or 3.0.9volume selection
3SerialEMimage acquisition
5RELION3.0.8CTF correction
8PHENIX1.18model fitting
11RELION3.0.8final Euler assignment
12RELION3.0.8classification
13RELION3.0.83D reconstruction
14PHENIX1.18model refinementreal-space refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 675 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 356 / Num. of volumes extracted: 77539
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

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

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
17OOC

7ooc

7OOC1
27OOD

7ood

7OOD2
34V7C

4v7c

84V7C3

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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