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- EMDB-70208: S. aureus YhaM D193A, 4 N-terminal domains, 2 RNA substrates -

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Basic information

Entry
Database: EMDB / ID: EMD-70208
TitleS. aureus YhaM D193A, 4 N-terminal domains, 2 RNA substrates
Map dataSharpened homogeneous refinement map, sharpened using PHENIX Autosharpen (sharpening B-factor 101.05 A^2)
Sample
  • Complex: YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substrates
    • Complex: YhaM D193A hexamer, 4 N-terminal domains
      • Protein or peptide: Cmp-binding-factor 1
    • Complex: RNA substrates
      • 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) / Streptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 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
DepositionApr 15, 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_70208.png

Downloads & links

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Map

FileDownload / File: emd_70208.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened homogeneous refinement map, sharpened using PHENIX Autosharpen (sharpening B-factor 101.05 A^2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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: 2.8
Minimum - Maximum-17.493880000000001 - 28.560452999999999
Average (Standard dev.)-0.000000000003278 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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_70208_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened homogeneous refinement map

Fileemd_70208_additional_1.map
AnnotationUnsharpened homogeneous refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Homogeneous refinement half map A

Fileemd_70208_half_map_1.map
AnnotationHomogeneous refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Homogeneous refinement half map B

Fileemd_70208_half_map_2.map
AnnotationHomogeneous refinement half map B
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, 4 N-terminal domains, 2 RNA substrates

EntireName: YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substrates
Components
  • Complex: YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substrates
    • Complex: YhaM D193A hexamer, 4 N-terminal domains
      • Protein or peptide: Cmp-binding-factor 1
    • Complex: RNA substrates
      • RNA: RNA
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substrates

SupramoleculeName: YhaM D193A hexamer, 4 N-terminal domains, 2 RNA substrates
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2

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Supramolecule #2: YhaM D193A hexamer, 4 N-terminal domains

SupramoleculeName: YhaM D193A hexamer, 4 N-terminal domains / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Supramolecule #3: RNA substrates

SupramoleculeName: RNA substrates / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Streptococcus pyogenes (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 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: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Streptococcus pyogenes (bacteria)
Molecular weightTheoretical: 8.125965 KDa
SequenceString:
AGGAAAAAAC AUUUUAUAAA GGAGA

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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

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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Homogeneous Refinement / Number images used: 78085
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 classificationSoftware - Name: cryoSPARC (ver. 4.5.3)
Software - details: cryoSPARC 3D classification (without particle alilgnments)
Details: YhaM particles with 2 NTDs per side of the hexameric ring (4 NTDs total) were isolated with 3 iterative 3D classification steps of 50 classes each, isolating particles with well-defined NTDs ...Details: YhaM particles with 2 NTDs per side of the hexameric ring (4 NTDs total) were isolated with 3 iterative 3D classification steps of 50 classes each, isolating particles with well-defined NTDs above and below the ring plane and finally identifying particles with exactly two NTDs per side.
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: 101 / Target criteria: Cross-correlation coefficient (CCmask)
Output model

PDB-9o7t:
S. aureus YhaM D193A, 4 N-terminal domains, 2 RNA substrates

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