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- EMDB-72981: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-72981
TitleCryo-EM structure of yeast Mgm101 bound to apparent B-form DNA
Map datastructure of yeast Mgm101 bound to apparent B-form DNA
Sample
  • Complex: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA
    • DNA: DNA (75+)
    • DNA: DNA (75-)
    • Protein or peptide: Mitochondrial genome maintenance protein MGM101
KeywordsSingle strand annealing protein / SSAP / annealase / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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) / Inovirus M13
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWheat CT / Bell CE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2212951 United States
CitationJournal: bioRxiv / Year: 2025
Title: Mechanism of single-strand annealing from native mass spectrometry and cryo-EM structures of RAD52 homolog Mgm101.
Authors: Carter T Wheat / Zihao Qi / Miqdad Hussain / Katerina Zakharova / Vicki H Wysocki / Charles E Bell /
Abstract: RAD52, the primary single-strand annealing (SSA) protein in humans, forms undecameric rings that bind ssDNA within a narrow, positively-charged groove. Whether RAD52 anneals two complementary ssDNAs ...RAD52, the primary single-strand annealing (SSA) protein in humans, forms undecameric rings that bind ssDNA within a narrow, positively-charged groove. Whether RAD52 anneals two complementary ssDNAs on the same ring in , or between two ring-ssDNA complexes in , is unknown. Here, we determined cryo-EM structures of Mgm101, a RAD52 homolog from yeast mitochondria, in complexes with ssDNA, a duplex intermediate of annealing, and B-form dsDNA product. In all states, Mgm101 forms a closed nonadecameric ring that binds the backbone of the first ssDNA at the base of the narrow groove. The second complementary strand binds directly on top of the first to form an extended, unwound, and circular duplex intermediate of annealing. The third complex captures apparent B-form DNA product bound to a novel β-hairpin motif located on top of the Mgm101 ring, above the primary DNA-binding groove. Mass photometry and native mass spectrometry confirm and further elucidate the complexes formed in solution. Altogether, our data reveal the full SSA pathway of Mgm101 and suggest it anneals two complementary ssDNAs on the same ring in . Structural conservation with RAD52 suggests it is likely to use a similar mechanism of annealing.
History
DepositionOct 1, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72981.png

Downloads & links

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Map

FileDownload / File: emd_72981.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of yeast Mgm101 bound to apparent B-form DNA
Projections & slices

Image control

Size
Brightness
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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: 0.0524
Minimum - Maximum-0.1322733 - 0.33605438
Average (Standard dev.)0.0005177745 (±0.012203522)
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_72981_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half Map B

Fileemd_72981_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72981_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA

EntireName: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA
Components
  • Complex: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA
    • DNA: DNA (75+)
    • DNA: DNA (75-)
    • Protein or peptide: Mitochondrial genome maintenance protein MGM101

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Supramolecule #1: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA

SupramoleculeName: Cryo-EM structure of yeast Mgm101 bound to apparent B-form DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 587 KDa

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Macromolecule #1: DNA (75+)

MacromoleculeName: DNA (75+) / type: dna / ID: 1
Details: The actual sequence is: TTGATAAGAGGTCATTTTTGCGGATGGCTTAGAGCTTAATTGCTGAATCTGGTGCTGTAGCTCAACATGTTTTAA
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Inovirus M13
Molecular weightTheoretical: 6.258394 KDa
SequenceString:
(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)

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Macromolecule #2: DNA (75-)

MacromoleculeName: DNA (75-) / type: dna / ID: 2
Details: The actual sequence is: TTAAAACATGTTGAGCTACAGCACCAGATTCAGCAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAA
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Inovirus M13
Molecular weightTheoretical: 6.618585 KDa
SequenceString:
(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN) (DN)(DN)(DN)(DN)(DN)(DN)(DN)(DN)

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Macromolecule #3: Mitochondrial genome maintenance protein MGM101

MacromoleculeName: Mitochondrial genome maintenance protein MGM101 / type: protein_or_peptide / ID: 3 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 40203
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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