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- PDB-9tze: 70S Coxiella burnetii Ribosome with Doxycycline and HPFcold -

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Basic information

Entry
Database: PDB / ID: 9tze
Title70S Coxiella burnetii Ribosome with Doxycycline and HPFcold
Components
  • (Large ribosomal subunit protein ...) x 29
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • Coxiellacae Large Subunit Peptide (CLaSP)
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / C. burnetii / 70S subunit / doxycycline / triple / stack / antibiotic / pathogen / hibernation factor / HPFcold / cold shock domain / ribosomal peptide / CLaSP / cryo-EM
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit ...negative regulation of translational elongation / ribosomal small subunit binding / assembly of large subunit precursor of preribosome / large ribosomal subunit / transferase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / nucleic acid binding / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain ...Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein S21 / Ribosomal protein L9 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L21, conserved site / : / Ribosomal protein L21 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / 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 L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / Ribosomal protein S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein L5, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / 30S ribosomal protein S17 / : / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein L16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L20 / Ribosomal protein S12, bacterial-type
Similarity search - Domain/homology
Chem-DXT / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 ...Chem-DXT / : / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL27 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12 / Ribosome hibernation promoting factor
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsStuart, W.S. / Isupov, M.N. / Harmer, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M009122/1 United Kingdom
CitationJournal: To Be Published
Title: 70S Coxiella burnetii Ribosome with Doxycycline and HPFcold
Authors: Stuart, W.S. / Isupov, M.N. / McLaren, M. / Jenkins, C.H. / Monier, A. / Daum, B. / Norville, I.H. / Gold, V.A.M. / Harmer, N.J.
History
DepositionJan 22, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Data collection / Source and taxonomy / Structure summary
Category: em_admin / entity ...em_admin / entity / entity_src_nat / pdbx_entity_src_syn
Item: _em_admin.last_update / _entity.src_method
Revision 1.1Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Experimental summary / Source and taxonomy / Structure summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: em_admin / entity ...em_admin / entity / entity_src_nat / pdbx_entity_src_syn
Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _entity.src_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 16S ribosomal RNA
C: Small ribosomal subunit protein uS3
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
F: Small ribosomal subunit protein bS6
G: Small ribosomal subunit protein uS7
H: Small ribosomal subunit protein uS8
I: Small ribosomal subunit protein uS9
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
L: Small ribosomal subunit protein uS12
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
O: Small ribosomal subunit protein uS15
P: Small ribosomal subunit protein bS16
Q: Small ribosomal subunit protein uS17
R: Small ribosomal subunit protein bS18
S: Small ribosomal subunit protein uS19
T: Small ribosomal subunit protein bS20
U: Small ribosomal subunit protein bS21
Z: Coxiellacae Large Subunit Peptide (CLaSP)
0: Large ribosomal subunit protein bL33
1: Large ribosomal subunit protein uL24
2: Large ribosomal subunit protein uL18
3: Large ribosomal subunit protein bL36
b: 5S ribosomal RNA
c: Large ribosomal subunit protein bL19
d: Large ribosomal subunit protein uL3
e: Large ribosomal subunit protein bL20
f: Large ribosomal subunit protein uL5
g: Large ribosomal subunit protein uL6
h: Large ribosomal subunit protein bL21
i: Large ribosomal subunit protein uL13
j: Large ribosomal subunit protein uL22
k: Large ribosomal subunit protein uL15
m: Large ribosomal subunit protein bL17
o: Large ribosomal subunit protein uL2
q: Large ribosomal subunit protein bL9
r: Large ribosomal subunit protein uL29
s: Large ribosomal subunit protein uL16
t: Large ribosomal subunit protein uL30
u: Large ribosomal subunit protein bL25
v: Large ribosomal subunit protein bL32
w: Large ribosomal subunit protein uL4
x: Large ribosomal subunit protein uL14
y: Large ribosomal subunit protein bL34
z: Large ribosomal subunit protein bL35
4: Large ribosomal subunit protein bL31
9: Ribosome hibernation promoting factor
8: Large ribosomal subunit protein bL27
7: Large ribosomal subunit protein uL23
6: Large ribosomal subunit protein bL28
a: 23S ribosomal RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,190,937446
Polymers2,177,53153
Non-polymers13,406393
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 3 types, 3 molecules Aba

#1: RNA chain 16S ribosomal RNA


Mass: 497437.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: GenBank: 2416246912
#26: RNA chain 5S ribosomal RNA


Mass: 37630.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: GenBank: 2294758066
#53: RNA chain 23S ribosomal RNA


Mass: 947544.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria)

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Small ribosomal subunit protein ... , 19 types, 19 molecules CDEFGHIJKLMNOPQRSTU

#2: Protein Small ribosomal subunit protein uS3 / 30S ribosomal protein S3


Mass: 25671.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: O85388
#3: Protein Small ribosomal subunit protein uS4 / 30S ribosomal protein S4


Mass: 23770.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EQ3
#4: Protein Small ribosomal subunit protein uS5 / 30S ribosomal protein S5


Mass: 17510.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EQ9
#5: Protein Small ribosomal subunit protein bS6 / 30S ribosomal protein S6


Mass: 14603.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83D76
#6: Protein Small ribosomal subunit protein uS7 / 30S ribosomal protein S7


Mass: 21334.717 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ES8
#7: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14592.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ER2
#8: Protein Small ribosomal subunit protein uS9 / 30S ribosomal protein S9


Mass: 15332.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83AX9
#9: Protein Small ribosomal subunit protein uS10 / 30S ribosomal protein S10


Mass: 12614.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ES5
#10: Protein Small ribosomal subunit protein uS11 / 30S ribosomal protein S11


Mass: 13534.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EQ4
#11: Protein Small ribosomal subunit protein uS12 / 30S ribosomal protein S12


Mass: 13786.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ES9
#12: Protein Small ribosomal subunit protein uS13 / 30S ribosomal protein S13


Mass: 13420.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: P59753
#13: Protein Small ribosomal subunit protein uS14


Mass: 11599.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ER3
#14: Protein Small ribosomal subunit protein uS15 / 30S ribosomal protein S15


Mass: 10340.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83D88
#15: Protein Small ribosomal subunit protein bS16 / 30S ribosomal protein S16


Mass: 15592.907 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83E83
#16: Protein Small ribosomal subunit protein uS17 / 30S ribosomal protein S17


Mass: 10328.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ER7
#17: Protein Small ribosomal subunit protein bS18 / 30S ribosomal protein S18


Mass: 8569.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83D75
#18: Protein Small ribosomal subunit protein uS19 / 30S ribosomal protein S19


Mass: 10842.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83ES0
#19: Protein Small ribosomal subunit protein bS20 / 30S ribosomal protein S20


Mass: 9981.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ED6
#20: Protein Small ribosomal subunit protein bS21 / 30S ribosomal protein S21


Mass: 8927.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83BB9

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Large ribosomal subunit protein ... , 29 types, 29 molecules 0123cdefghijkmoqrstuvwxyz4876

#22: Protein Large ribosomal subunit protein bL33 / 50S ribosomal protein L33


Mass: 8054.479 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EM5
#23: Protein Large ribosomal subunit protein uL24 / 50S ribosomal protein L24


Mass: 11814.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ER5
#24: Protein Large ribosomal subunit protein uL18 / 50S ribosomal protein L18


Mass: 13137.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: UniProt: Q83ER0
#25: Protein/peptide Large ribosomal subunit protein bL36 / 50S ribosomal protein L36


Mass: 4668.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q4AAY2
#27: Protein Large ribosomal subunit protein bL19 / 50S ribosomal protein L19


Mass: 13302.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83E85
#28: Protein Large ribosomal subunit protein uL3 / 50S ribosomal protein L3


Mass: 23547.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J263
#29: Protein Large ribosomal subunit protein bL20 / 50S ribosomal protein L20


Mass: 13475.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83C13
#30: Protein Large ribosomal subunit protein uL5 / 50S ribosomal protein L5


Mass: 20782.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ER4
#31: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19228.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5E7
#32: Protein Large ribosomal subunit protein bL21 / 50S ribosomal protein L21


Mass: 12785.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83EE0
#33: Protein Large ribosomal subunit protein uL13 / 50S ribosomal protein L13


Mass: 15840.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J4G5
#34: Protein Large ribosomal subunit protein uL22 / 50S ribosomal protein L22


Mass: 12605.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J258
#35: Protein Large ribosomal subunit protein uL15 / 50S ribosomal protein L15


Mass: 15320.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J244
#36: Protein Large ribosomal subunit protein bL17 / 50S ribosomal protein L17


Mass: 14574.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J237
#37: Protein Large ribosomal subunit protein uL2 / 50S ribosomal protein L2


Mass: 30481.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J260
#38: Protein Large ribosomal subunit protein bL9 / 50S ribosomal protein L9


Mass: 16603.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: A9ND50
#39: Protein Large ribosomal subunit protein uL29 / 50S ribosomal protein L29


Mass: 7717.034 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5E0
#40: Protein Large ribosomal subunit protein uL16 / 50S ribosomal protein L16


Mass: 15532.356 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J256
#41: Protein Large ribosomal subunit protein uL30 / 50S ribosomal protein L30


Mass: 7312.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5F0
#42: Protein Large ribosomal subunit protein bL25 / 50S ribosomal protein L25 / General stress protein CTC


Mass: 26577.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J9D8
#43: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 7486.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J8E7
#44: Protein Large ribosomal subunit protein uL4 / 50S ribosomal protein L4


Mass: 22409.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: A9NAM5
#45: Protein Large ribosomal subunit protein uL14 / 50S ribosomal protein L14


Mass: 13564.108 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5E2
#46: Protein/peptide Large ribosomal subunit protein bL34 / 50S ribosomal protein L34


Mass: 5357.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J2B1
#47: Protein Large ribosomal subunit protein bL35 / 50S ribosomal protein L35


Mass: 7415.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J7Y0
#48: Protein Large ribosomal subunit protein bL31 / 50S ribosomal protein L31


Mass: 9096.483 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83D39
#50: Protein Large ribosomal subunit protein bL27 / 50S ribosomal protein L27


Mass: 10069.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J9K3
#51: Protein Large ribosomal subunit protein uL23 / 50S ribosomal protein L23


Mass: 10828.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83ES2
#52: Protein Large ribosomal subunit protein bL28 / 50S ribosomal protein L28


Mass: 9266.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: B6J5S6

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Protein/peptide / Protein , 2 types, 2 molecules Z9

#21: Protein/peptide Coxiellacae Large Subunit Peptide (CLaSP)


Mass: 2530.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria)
#49: Protein Ribosome hibernation promoting factor / Hibernation factor HPF


Mass: 21176.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / References: UniProt: Q83FC0

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Non-polymers , 5 types, 408 molecules

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


Mass: 24.305 Da / Num. of mol.: 220 / Source method: obtained synthetically / Formula: Mg
#55: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 167 / Source method: obtained synthetically / Formula: K
#56: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#57: Chemical ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#58: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: Coxiella burnetii 70S Ribosome / Type: RIBOSOME / Entity ID: #1-#53 / Source: NATURAL
Source (natural)Organism: Coxiella burnetii (bacteria) / Strain: NMII
Buffer solutionpH: 7.5 / Details: BS100 ribosomal resuspension buffer
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2100 mMPotassium Acetate251
315 mMMagnesium AcetateMg(OAc)1
41 mMDTTC4H10O2S21
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K / Details: Blot time 4 s, blot force 1, blot total 1

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Super-resolution binned 2 in EPU
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: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 34720
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2cryoSPARC4particle selection
3EPUimage acquisition
5cryoSPARC4CTF correction
8UCSF ChimeraX1.9model fitting
9ISOLDEmodel fitting
10Cootmodel fitting
12REFMACmodel refinement
14cryoSPARC4final Euler assignment
15cryoSPARC4classification
16cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44196 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDSource nameTypeDetails (eV)
11AlphaFoldin silico model
21Otherin silico modelModel Angelo

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