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- EMDB-73296: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-73296
TitleS. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
Map dataSharpened map from cryoSPARC Non-Uniform Refinement (Bsharpen = -102.0 A^2)
Sample
  • Complex: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
    • Complex: YhaM D193A hexamer
      • Protein or peptide: Cmp-binding-factor 1
    • Complex: hairpin RNA substrate
      • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
Keywordsexonuclease / 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
Cmp-binding-factor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMattingly JM / Tanquary JR / Dunham CM
Funding support United States, 4 items
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, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73296.png

Downloads & links

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Map

FileDownload / File: emd_73296.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from cryoSPARC Non-Uniform Refinement (Bsharpen = -102.0 A^2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å		0.73 Å/pix.
x 300 pix.
= 219. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039
Minimum - Maximum-0.11485425 - 0.2435798
Average (Standard dev.)0.0015847466 (±0.009592248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 219.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73296_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryoSPARC Non-Uniform Refinement map

Fileemd_73296_additional_1.map
AnnotationUnsharpened cryoSPARC Non-Uniform Refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked, unfiltered half-map from cryoSPARC Non-Uniform Refinement

Fileemd_73296_half_map_1.map
AnnotationUnmasked, unfiltered half-map from cryoSPARC Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked, unfiltered half-map from cryoSPARC Non-Uniform Refinement

Fileemd_73296_half_map_2.map
AnnotationUnmasked, unfiltered half-map from cryoSPARC Non-Uniform Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate

EntireName: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
Components
  • Complex: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
    • Complex: YhaM D193A hexamer
      • Protein or peptide: Cmp-binding-factor 1
    • Complex: hairpin RNA substrate
      • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate

SupramoleculeName: S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2

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Supramolecule #2: YhaM D193A hexamer

SupramoleculeName: YhaM D193A hexamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Supramolecule #3: hairpin RNA substrate

SupramoleculeName: hairpin RNA substrate / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Staphylococcus aureus (bacteria) / Synthetically produced: Yes

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Macromolecule #1: Cmp-binding-factor 1

MacromoleculeName: Cmp-binding-factor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 35.785797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRNIENLNPG DSVDHFFLVH KATQGVTAQG KDYMTLHLQD KSGEIEAKFW TATKNDMATI KPEEIVHVKG DIINYRGNKQ MKVNQIRLA TTEDQLKTEQ FVDGAPLSPA EIQEEISHYL LDIENANLQR ITRHLLKKYQ ERFYTYPAAS SHHHNFASGL S YHVLTMLR ...String:
MRNIENLNPG DSVDHFFLVH KATQGVTAQG KDYMTLHLQD KSGEIEAKFW TATKNDMATI KPEEIVHVKG DIINYRGNKQ MKVNQIRLA TTEDQLKTEQ FVDGAPLSPA EIQEEISHYL LDIENANLQR ITRHLLKKYQ ERFYTYPAAS SHHHNFASGL S YHVLTMLR IAKSICDIYP LLNKSLLYSG IILHAIGKVR ELSGPVATSY TVEGNLLGHI SIASDEVVEA ARELNIEGEE IM LLRHMIL SHHGKLEYGS PKLPYLKEAE ILCYIDNIDA RMNMFEKAYK KTDKGQFTDK IFGLENRRFY NPESLD

UniProtKB: Cmp-binding-factor 1

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 12.636384 KDa
SequenceString:
UAAAGCACUU GUGUUUUUGC ACAAGUGCUU UUUUAUACUC

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNaH2PO4sodium dihydrogen phosphate
150.0 mMNaClsodium chloride
7.0 mMMgCl2magnesium chloride
1.0 % v/vC3H8O3glycerol
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 15724 / Average exposure time: 6.0 sec. / Average electron dose: 52.97 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2080911
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryoSPARC Ab-Initio Reconstruction with 5 classes
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Homogeneous Reconstruct Only / Number images used: 42145
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Non-Uniform Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Non-Uniform Refinement
Final 3D classificationNumber classes: 4 / Avg.num./class: 14733 / Software - Name: cryoSPARC (ver. 4.7.0)
Software - details: cryoSPARC 3D Classication (without alignment)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: Initial model generated de novo using ModelAngelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 102
Output model

PDB-9ypf:
S. aureus YhaM D193A hexamer, 3 NTDs, hairpin RNA substrate

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