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- EMDB-70886: S. aureus YhaM D193A hexamer, D3 refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-70886
TitleS. aureus YhaM D193A hexamer, D3 refinement
Map dataSharpened Homogeneous Refinement map, used for modeling. Bsharpen = 126.9
Sample
  • Complex: YhaM D193A hexamer
    • Protein or peptide: YhaM
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
Keywordsexonuclease / translation / RNA / RNA BINDING PROTEIN
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: 2.36 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
DepositionMay 29, 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_70886.png

Downloads & links

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Map

FileDownload / File: emd_70886.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Homogeneous Refinement map, used for modeling. Bsharpen = 126.9
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.45829648 - 0.8033621
Average (Standard dev.)0.00011841446 (±0.027426746)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70886_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map from Homogeneous Refinement

Fileemd_70886_additional_1.map
AnnotationUnsharpened map from Homogeneous Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A from Homogeneous Refinement

Fileemd_70886_half_map_1.map
AnnotationHalf-map A from Homogeneous Refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B from Homogeneous Refinement

Fileemd_70886_half_map_2.map
AnnotationHalf-map B from Homogeneous 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 : YhaM D193A hexamer

EntireName: YhaM D193A hexamer
Components
  • Complex: YhaM D193A hexamer
    • Protein or peptide: YhaM
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: YhaM D193A hexamer

SupramoleculeName: YhaM D193A hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: YhaM

MacromoleculeName: YhaM / 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 BL21(DE3) (bacteria)
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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 3 / 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

Concentration1.1 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 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
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: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 14007 / Average exposure time: 1.6 sec. / Average electron dose: 47.0 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: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
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: 8389618
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Software - details: Patch CTF Estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: cryoSPARC ab-initio reconstruction
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D3 (2x3 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Homogeneous Refinement / Number images used: 3124511
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Homogeneous Refinement / Details: cryoSPARC homogeneous refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Homogeneous Refinement / Details: cryoSPARC homogeneous refinement
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: cryoSPARC heterogeneous refinement
Details: YhaM hexamer particles were separated from junk using a cryoSPARC heterogeneous refinement job with a YhaM hexamer volume and junk volume as inputs
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 built de novo using ModelAngelo
DetailsModel was built into main EM map de novo using ModelAngelo, then flexibly fit using PHENIX real-space model refinement.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 126.9 / Target criteria: Cross-correlation coefficient (CCmask)
Output model

PDB-9ov1:
S. aureus YhaM D193A hexamer, D3 refinement

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