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- EMDB-51819: Cryo-EM structure of YhaM -

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Basic information

Entry
Database: EMDB / ID: EMD-51819
TitleCryo-EM structure of YhaM
Map data
Sample
  • Complex: YhaM
    • Protein or peptide: 3'-5' exoribonuclease YhaM
  • Ligand: MAGNESIUM ION
Keywords3'-5' exoribonuclease / DNA BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsPane-Farre J / Madej MG / Fu L / Ziegler C / Hinrichs R
Funding support1 items
OrganizationGrant numberCountry
Other governmentSYN/5/2023
CitationJournal: 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, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51819.png

Downloads & links

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Map

FileDownload / File: emd_51819.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 320 pix.
= 252.512 Å		0.79 Å/pix.
x 320 pix.
= 252.512 Å		0.79 Å/pix.
x 320 pix.
= 252.512 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.411
Minimum - Maximum-4.0231624 - 6.3119664
Average (Standard dev.)-0.0014158448 (±0.13074367)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 252.512 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51819_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51819_half_map_2.map
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

EntireName: YhaM
Components
  • Complex: YhaM
    • Protein or peptide: 3'-5' exoribonuclease YhaM
  • Ligand: MAGNESIUM ION

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Supramolecule #1: YhaM

SupramoleculeName: YhaM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacillus subtilis (bacteria)

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Macromolecule #1: 3'-5' exoribonuclease YhaM

MacromoleculeName: 3'-5' exoribonuclease YhaM / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 36.617926 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGAKGIMLHE VGEQVDQYLL IKSSTKGIAS NGKPFLTLML QDQSGDIEAK LWDAKQSDEV TYAPQTIVKV VGDVHHYRGR TQLKLRNIR PVSEQENVNI DDFLETAPIP KNEMMDTITQ YIFEMKNPNI QRITRFLVKK HEAEFMDYPA ATKNHHEFVS G LAYHVVSM ...String:
MGAKGIMLHE VGEQVDQYLL IKSSTKGIAS NGKPFLTLML QDQSGDIEAK LWDAKQSDEV TYAPQTIVKV VGDVHHYRGR TQLKLRNIR PVSEQENVNI DDFLETAPIP KNEMMDTITQ YIFEMKNPNI QRITRFLVKK HEAEFMDYPA ATKNHHEFVS G LAYHVVSM LNLAKAIADL YPSLDRDLLY AGVILHDLGK VKELSGPVST SYTVEGNLLG HISIMVTELS KAAEELQIDS EE VLILQHL ILSHHGKAEW GSPKPPMVKE AEILHYIDNL DAKMNMMDRA LERVKPGEYT ERVFALENRS FYKPTFHKHH HHH H

UniProtKB: 3'-5' exoribonuclease YhaM

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationName
25.0 mMTRIS
200.0 mMNaCl
20.0 mMMagnesium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.21 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER

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Image processing

Particle selectionNumber selected: 3338722
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AF-O07521-F1-v4
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1168864
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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