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- PDB-9t61: Doxycycline Bound C. burnetii 30S Ribosome -

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Basic information

Entry
Database: PDB / ID: 9t61
TitleDoxycycline Bound C. burnetii 30S Ribosome
Components
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • Large ribosomal subunit protein bL31
  • P-site tRNA-Met
KeywordsRIBOSOME / C. burnetii / 30S subunit / antibiotic / doxycycline / pathogen / cryo-EM
Function / homology
Function and homology information


ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation ...ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 S3, bacterial-type ...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 S3, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S19, 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 S4, bacterial-type / Ribosomal protein S5, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / L28p-like / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / K Homology domain / K homology RNA-binding domain / Ribosomal protein S18 superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / : / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S7, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7 signature. / K homology domain superfamily, prokaryotic type / : / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S8 signature. / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / K homology domain-like, alpha/beta / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal protein S13-like, H2TH / Ribosomal protein S10p/S20e / S4 RNA-binding domain / S4 domain / Ribosomal S11, conserved site / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S11 signature.
Similarity search - Domain/homology
Chem-DXT / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 ...Chem-DXT / : / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein bS21 / 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 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS12
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 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: To be confirmed on publication
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
DepositionNov 6, 2025Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
4: Large ribosomal subunit protein bL31
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
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
Y: P-site tRNA-Met
J: Small ribosomal subunit protein uS10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)806,854113
Polymers803,63722
Non-polymers3,21791
Water1448
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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Protein , 1 types, 1 molecules 4

#1: 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) / Strain: NMII / References: UniProt: Q83D39

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RNA chain , 2 types, 2 molecules AY

#2: 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) / Strain: NMII
#21: RNA chain P-site tRNA-Met


Mass: 24749.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Coxiella burnetii (bacteria) / Strain: NMII / References: GenBank: 2294758066

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

#3: 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) / Strain: NMII / References: UniProt: O85388
#4: 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) / Strain: NMII / References: UniProt: Q83EQ3
#5: 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) / Strain: NMII / References: UniProt: Q83EQ9
#6: 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
#7: 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) / Strain: NMII / References: UniProt: Q83ES8
#8: 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) / Strain: NMII / References: UniProt: Q83ER2
#9: 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) / Strain: NMII / References: UniProt: Q83AX9
#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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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) / Strain: NMII / 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
#22: 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) / Strain: NMII / References: UniProt: Q83ES5

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Non-polymers , 5 types, 99 molecules

#23: 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.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: K
#25: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: Mg
#26: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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

Component
IDNameTypeEntity IDParent-IDSource
1Coxiella Ribosome 30S SubunitRIBOSOME#1-#9, #22, #10-#210NATURAL
216S rRNACOMPLEX#21NATURAL
3Ribosomal ProteinCOMPLEX#1, #3-#9, #22, #10-#201NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Coxiella burnetii (bacteria)777NMII
32Coxiella burnetii (bacteria)777NMII
43Coxiella burnetii (bacteria)777NMII
Buffer solutionpH: 7.5 / Details: BS100 ribosomal resuspension buffer
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2100 mMPotassium AcetateKOAc1
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 recordingAverage exposure time: 3 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 22295
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2cryoSPARC4particle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraX1.9model fitting
9ISOLDEmodel fitting
10Cootmodel fitting
12cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
14cryoSPARCclassification
15cryoSPARC43D reconstruction
16REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10803 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDSource nameTypeDetails (eV)
11AlphaFoldin silico model
21Otherin silico modelModel Angelo

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