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

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Basic information

Entry
Database: PDB / ID: 9ov1
TitleS. aureus YhaM D193A hexamer, D3 refinement
ComponentsYhaM
KeywordsRNA BINDING PROTEIN / exonuclease / translation / RNA
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 / Cmp-binding-factor 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.36 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: To Be Published
Title: Structural insights into RNA recognition by the Staphylococcus aureus exoribonuclease YhaM
Authors: Mattingly, J.M. / Tanquary, J.R. / Liponska, A. / Yap, M.N.F. / Dunham, C.M.
History
DepositionMay 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 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

Downloads & links

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Assembly

Deposited unit
A: YhaM
B: YhaM
C: YhaM
D: YhaM
E: YhaM
F: YhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,57624
Polymers214,7156
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
YhaM / 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 BL21(DE3) (bacteria) / References: UniProt: A0A0H2XHZ3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: 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

ComponentName: YhaM D193A hexamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium dihydrogen phosphateNaH2PO41
2150 mMsodium chlorideNaCl1
37 mMmagnesium chlorideMgCl21
41 % v/vglycerolC3H8O31
SpecimenConc.: 1.1 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: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.6 sec. / Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14007
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topaz0.2.5particle selection
2Leginonimage acquisition
4cryoSPARC4.5.3CTF correctionPatch CTF Estimation
9PHENIXmodel refinement
10cryoSPARC4.5.3initial Euler assignmentHomogeneous Refinement
11cryoSPARC4.5.3final Euler assignmentHomogeneous Refinement
12cryoSPARC4.5.3classificationcryoSPARC heterogeneous refinement
13cryoSPARC4.5.33D reconstructionHomogeneous Refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8389618
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3124511 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 126.9 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient (CCmask)
Details: Model was built into main EM map de novo using ModelAngelo, then flexibly fit using PHENIX real-space model refinement.
Atomic model buildingDetails: Initial model built de novo using ModelAngelo / Source name: Other / Type: other

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