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- EMDB-73295: S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-73295
TitleS. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate
Map dataSharpened map from cryoSPARC Non-Uniform Refinement (Bsharpen = -129.7 A^2)
Sample
  • Complex: S. aureus YhaM D193A hexamer, 2 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: 3.2 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: To Be Published
Title: Structural insights into RNA recognition by the Staphylococcus aureus exoribonuclease YhaM
Authors: Mattingly JM / Tanquary JR / Liponska A / Yap MNF / Dunham CM
History
DepositionOct 14, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73295.png

Downloads & links

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Map

FileDownload / File: emd_73295.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map from cryoSPARC Non-Uniform Refinement (Bsharpen = -129.7 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: 0.06
Minimum - Maximum-0.17368935 - 0.33729684
Average (Standard dev.)0.0014987917 (±0.011793284)
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_73295_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_73295_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_73295_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_73295_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, 2 NTDs, hairpin RNA substrate

EntireName: S. aureus YhaM D193A hexamer, 2 NTDs, hairpin RNA substrate
Components
  • Complex: S. aureus YhaM D193A hexamer, 2 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, 2 NTDs, hairpin RNA substrate

SupramoleculeName: S. aureus YhaM D193A hexamer, 2 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: 15 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Software - details: Non-Uniform Refinement / Number images used: 224020
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: 16 / Avg.num./class: 14925 / 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: 129.7
Output model

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

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