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- PDB-9h3f: Cryo-EM structure of YhaM -

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Basic information

Entry
Database: PDB / ID: 9h3f
TitleCryo-EM structure of YhaM
Components3'-5' exoribonuclease YhaM
KeywordsDNA BINDING PROTEIN / 3'-5' exoribonuclease
Function / homology
Function and homology information


rRNA 3'-end processing / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / DNA binding
Similarity search - Function
3'-5' exoribonuclease YhaM / : / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
3'-5' exoribonuclease YhaM
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsPane-Farre, J. / Madej, M.G. / Fu, L. / Ziegler, C. / Hinrichs, R.
Funding support1items
OrganizationGrant numberCountry
Other governmentSYN/5/2023
Citation
Journal: Nucleic Acids Res / Year: 2025
Title: A conserved nuclease facilitates environmental DNA uptake.
Authors: Juri Hanßmann / Jan Pané-Farré / Milena Meiser / Mathias Girbig / Lifei Fu / M Gregor Madej / Franziska L Sendker / Clemens Thölken / Marcus Lechner / Christine Ziegler / Georg K A ...Authors: Juri Hanßmann / Jan Pané-Farré / Milena Meiser / Mathias Girbig / Lifei Fu / M Gregor Madej / Franziska L Sendker / Clemens Thölken / Marcus Lechner / Christine Ziegler / Georg K A Hochberg / Gert Bange / Martin Thanbichler / Rebecca Hinrichs /
Abstract: Bacteria acquire new traits through the uptake of genetic material from the environment, a process requiring DNA processing. However, the molecular inventory mediating this process is far from being ...Bacteria acquire new traits through the uptake of genetic material from the environment, a process requiring DNA processing. However, the molecular inventory mediating this process is far from being completely understood. Here, we identify YhaM in Bacillus subtilis as a conserved 3'-deoxyribonuclease essential for the uptake and processing of genetic information in the form of single-stranded DNA. Our results show that YhaM assembles into hexamers in the presence of divalent cations, enhancing substrate binding, which is achieved through its conserved oligonucleotide-binding domain. Cells lacking YhaM show a severe defect in the uptake of plasmids and genomic DNA, but the transduction of double-stranded DNA by the phage SPP1 remains unaffected. These findings highlight a critical role of YhaM in single-stranded DNA maturation during natural transformation. Importantly, this function is conserved in various Gram-positive human pathogens such as Staphylococcus aureus, suggesting that it could contribute to the spread of antibiotic resistance.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3'-5' exoribonuclease YhaM
B: 3'-5' exoribonuclease YhaM
C: 3'-5' exoribonuclease YhaM
D: 3'-5' exoribonuclease YhaM
E: 3'-5' exoribonuclease YhaM
F: 3'-5' exoribonuclease YhaM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,99918
Polymers219,7086
Non-polymers29212
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
3'-5' exoribonuclease YhaM


Mass: 36617.926 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhaM, BSU09930 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O07521, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
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 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
125 mMTRIS1
2200 mMNaCl1
320 mMMagnesium chloride1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: JEOL CRYOSPECPORTER
Image recordingElectron dose: 57.21 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
2PHENIXmodel refinement
3SerialEMimage acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3338722
3D reconstructionResolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1168864 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510440
ELECTRON MICROSCOPYf_angle_d0.86814124
ELECTRON MICROSCOPYf_dihedral_angle_d5.1451368
ELECTRON MICROSCOPYf_chiral_restr0.0531578
ELECTRON MICROSCOPYf_plane_restr0.0061806

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