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- PDB-9ype: S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate -

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Basic information

Entry
Database: PDB / ID: 9ype
TitleS. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate
Components
  • Cmp-binding-factor 1
  • RNA
KeywordsRNA BINDING PROTEIN/RNA / exonuclease / translation / RNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


rRNA 3'-end processing / exonuclease activity / nucleic acid binding
Similarity search - Function
: / HD domain profile. / HD domain / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
PHOSPHATE ION / RNA / RNA (> 10) / Cmp-binding-factor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMattingly, J.M. / Tanquary, J.R. / Dunham, C.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM121359 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI150986 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093278 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM8367 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural insights into RNA recognition by the exoribonuclease YhaM.
Authors: Jacob M Mattingly / Anna Lipońska / Julia Tanquary / Mee-Ngan F Yap / Christine M Dunham /
Abstract: Bacterial ribonucleases regulate gene expression in response to environmental stress and host interactions. In the hibernation-promoting factor (Hpf) induces the formation of RNase R-resistant 100S ...Bacterial ribonucleases regulate gene expression in response to environmental stress and host interactions. In the hibernation-promoting factor (Hpf) induces the formation of RNase R-resistant 100S ribosomes. We previously showed that the 3'-5' exoribonuclease YhaM cleaves the transcript, reducing Hpf synthesis and leading to ribosome degradation. No structure of any YhaM homolog bound to RNA is available, and biological investigations of YhaM remain limited. Here, we find that deletion of attenuates virulence in a infection model. We further determined electron cryomicroscopy structures of YhaM-RNA complexes. YhaM adopts a hexameric complex arranged in a ring, with its N-terminal oligonucleotide/oligosaccharide-binding (OB) domains positioned on both sides of the ring while the catalytic histidine/aspartate-rich (HD) domain active sites are buried within the interior. The OB-1'' domains recognize the hairpin by the formation of complementary minor groove interactions. RNA binding by two YhaM OB domains is mediated through engagement of both the backbones and nucleobases of the RNA substrate, where stacking of aromatic residues and nucleobases likely contributes to substrate recognition. Structures of YhaM bound to a single-stranded RNA reveal how the 3' ends of two RNAs are positioned within the HD domain poised for catalysis. Although six YhaM active sites are present, only two engage in RNA cleavage and further point to the importance of the remaining YhaM monomers as structural scaffolds for guiding RNA to the active site. In summary, these findings provide insights into the unique assembly of an understudied bacterial RNase.
History
DepositionOct 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cmp-binding-factor 1
B: Cmp-binding-factor 1
C: Cmp-binding-factor 1
D: Cmp-binding-factor 1
E: Cmp-binding-factor 1
F: Cmp-binding-factor 1
G: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,21325
Polymers227,3517
Non-polymers86118
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Cmp-binding-factor 1


Mass: 35785.797 Da / Num. of mol.: 6 / Mutation: D193A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cbf1, SAUSA300_1791 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XHZ3
#2: RNA chain RNA


Mass: 12636.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
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
1S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrateCOMPLEX#20MULTIPLE SOURCES
2YhaM D193A hexamerCOMPLEX#11RECOMBINANT
3hairpin RNA substrateCOMPLEX#21SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Staphylococcus aureus (bacteria)1280
33Staphylococcus aureus (bacteria)1280
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium dihydrogen phosphateNaH2PO41
2150 mMsodium chlorideNaCl1
37 mMmagnesium chlorideMgCl21
41 % v/vglycerolC3H8O31
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 52.97 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15724
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARC4.7.0particle selectioncryoSPARC Template Picker (following micrograph denoising with Micrograph Denoiser)
2Leginonimage acquisition
4cryoSPARC4.7.0CTF correctionPatch CTF Estimation
7UCSF ChimeraXmodel fitting
9cryoSPARC4.7.0initial Euler assignmentNon-Uniform Refinement
10cryoSPARC4.7.0final Euler assignmentNon-Uniform Refinement
11cryoSPARC4.7.0classificationcryoSPARC 3D Classication (without alignment)
12cryoSPARC4.7.03D reconstructionNon-Uniform Refinement
19PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2080911
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224020 / Algorithm: BACK PROJECTION / Num. of class averages: 15 / Symmetry type: POINT
Atomic model buildingB value: 129.7 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Initial model generated de novo using ModelAngelo / Source name: Other / Type: other

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