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- EMDB-72984: Cryo-EM structure of yeast Mgm101 in the ring apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-72984
TitleCryo-EM structure of yeast Mgm101 in the ring apo state
Map datastructure of yeast Mgm101 in the ring apo state
Sample
  • Complex: Cryo-EM structure of yeast Mgm101 in the ring apo state
    • Protein or peptide: Mitochondrial genome maintenance protein MGM101
KeywordsSingle strand annealing protein / SSAP / annealase / DNA BINDING PROTEIN
Function / homology
Function and homology information


mitochondrial chromosome / : / recombinational repair / mitochondrial nucleoid / interstrand cross-link repair / single-stranded DNA binding / DNA repair / mitochondrion / DNA binding
Similarity search - Function
Mitochondrial genome maintenance protein Mgm101 / Mitochondrial genome maintenance MGM101
Similarity search - Domain/homology
Mitochondrial genome maintenance protein MGM101
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsWheat CT / Bell CE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2212951 United States
CitationJournal: To Be Published
Title: Mechanism of single-strand annealing from native mass spectrometry and cryo-EM structures of RAD52 homolog Mgm101
Authors: Wheat CT / Bell CE
History
DepositionOct 1, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72984.png

Downloads & links

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Map

FileDownload / File: emd_72984.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of yeast Mgm101 in the ring apo state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.904 Å		0.85 Å/pix.
x 352 pix.
= 299.904 Å		0.85 Å/pix.
x 352 pix.
= 299.904 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0577
Minimum - Maximum-0.0018867332 - 1.5030867
Average (Standard dev.)0.001796878 (±0.028969092)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_72984_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72984_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72984_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of yeast Mgm101 in the ring apo state

EntireName: Cryo-EM structure of yeast Mgm101 in the ring apo state
Components
  • Complex: Cryo-EM structure of yeast Mgm101 in the ring apo state
    • Protein or peptide: Mitochondrial genome maintenance protein MGM101

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Supramolecule #1: Cryo-EM structure of yeast Mgm101 in the ring apo state

SupramoleculeName: Cryo-EM structure of yeast Mgm101 in the ring apo state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 541 KDa

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Macromolecule #1: Mitochondrial genome maintenance protein MGM101

MacromoleculeName: Mitochondrial genome maintenance protein MGM101 / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.524535 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPKVPEFGSV VSTGTSNTAT AGAVRKSFNS TETKPVFATK SEAGNGSHMK EYSSGINSKL GGTPLETRST ADDSLNNSYK QVKGDIDWY TSWYGLGMKP FEAKVQKDLI EPLDPKDIEI KPDGLIYLPE IKYRRILNKA FGAGGWGLVP RSQTIVTSKL V TREYGLIC ...String:
GPKVPEFGSV VSTGTSNTAT AGAVRKSFNS TETKPVFATK SEAGNGSHMK EYSSGINSKL GGTPLETRST ADDSLNNSYK QVKGDIDWY TSWYGLGMKP FEAKVQKDLI EPLDPKDIEI KPDGLIYLPE IKYRRILNKA FGAGGWGLVP RSQTIVTSKL V TREYGLIC HGQLISVARG EQDYFNEAGI PTATEGCKSN ALMRCCKDLG VGSELWDPVF IKKFKVDHCT EKFVEHVTTK RK KKIWLRK DRQVEYPYK

UniProtKB: Mitochondrial genome maintenance protein MGM101

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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: 7.5
VitrificationCryogen name: ETHANE

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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 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C19 (19 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 383000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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