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- PDB-9t0z: HPFcold Bound Hibernating C. burnetii 30S Ribosome -

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Basic information

Entry
Database: PDB / ID: 9t0z
TitleHPFcold Bound Hibernating C. burnetii 30S Ribosome
Components
  • (Small ribosomal subunit protein ...) x 19
  • 16S ribosomal RNA
  • Large ribosomal subunit protein bL31
  • Ribosome hibernation promoting factor
KeywordsRIBOSOME / C. burnetii / 30S subunit / cold shock domain / pathogen / ribosomal peptide / hibernation / cryo-EM
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / tRNA binding / rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / ribosome biogenesis / ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / tRNA binding / 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 S14, bacterial/plastid / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 ...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 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
Similarity search - Domain/homology
: / 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 ...: / 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 / Ribosome hibernation promoting factor
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 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: HPFcold Bound Hibernating C. burnetii 30S Ribosome
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
DepositionOct 20, 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

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Assembly

Deposited unit
M: Small ribosomal subunit protein uS13
N: Small ribosomal subunit protein uS14
9: Ribosome hibernation promoting factor
S: Small ribosomal subunit protein uS19
A: 16S ribosomal RNA
O: Small ribosomal subunit protein uS15
C: Small ribosomal subunit protein uS3
I: Small ribosomal subunit protein uS9
U: Small ribosomal subunit protein bS21
F: Small ribosomal subunit protein bS6
T: Small ribosomal subunit protein bS20
D: Small ribosomal subunit protein uS4
E: Small ribosomal subunit protein uS5
H: Small ribosomal subunit protein uS8
P: Small ribosomal subunit protein bS16
L: Small ribosomal subunit protein uS12
Q: Small ribosomal subunit protein uS17
4: Large ribosomal subunit protein bL31
G: Small ribosomal subunit protein uS7
J: Small ribosomal subunit protein uS10
K: Small ribosomal subunit protein uS11
R: Small ribosomal subunit protein bS18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)802,812111
Polymers800,06422
Non-polymers2,74889
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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Small ribosomal subunit protein ... , 19 types, 19 molecules MNSOCIUFTDEHPLQGJKR

#1: 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
#2: 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
#4: 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
#6: 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
#7: 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
#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) / Strain: NMII / References: UniProt: Q83AX9
#9: 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) / Strain: NMII / References: UniProt: Q83BB9
#10: 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) / Strain: NMII / References: UniProt: Q83D76
#11: 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
#12: 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
#13: 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
#14: 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
#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 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
#17: 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
#19: 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
#20: 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
#21: 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
#22: 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

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Protein , 2 types, 2 molecules 94

#3: 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) / Strain: NMII / References: UniProt: Q83FC0
#18: 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 , 1 types, 1 molecules A

#5: 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

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Non-polymers , 4 types, 97 molecules

#23: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 53 / Source method: obtained synthetically / Formula: Mg
#26: 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 interestN
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 50S SubunitRIBOSOME#1-#220NATURAL
216SCOMPLEX#17-#221NATURAL
3Ribosomal ProteinCOMPLEX1NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.34 MDaNO
21NO
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
5cryoSPARC4CTF correction
8UCSF ChimeraX1.9model fitting
9ISOLDEmodel fitting
10Cootmodel fitting
12cryoSPARC4initial Euler assignment
14cryoSPARC4classification
15cryoSPARC43D reconstruction
16REFMAC5.8.0258model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24143 / Symmetry type: POINT
Atomic model building
ID 3D fitting-IDSource nameTypeDetails (eV)
11AlphaFoldin silico model
21Otherin silico modelModel Angelo
RefinementResolution: 2.87→424 Å / Cor.coef. Fo:Fc: 0.764
RfactorNum. reflection% reflection
Rwork0.50765 --
obs0.50765 6752605 100 %
Displacement parametersBiso mean: 61.563 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å2-1.4 Å20.73 Å2
2--2.86 Å21.19 Å2
3----0.74 Å2
LS refinement shellHighest resolution: 2.87 Å /
Rfactor% reflection
Rfree0 -
Rwork0.871 -
obs-100 %

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