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- PDB-9yi9: Cryo-EM structure of yeast Mgm101 in the lock-washer apo state -

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Basic information

Entry
Database: PDB / ID: 9yi9
TitleCryo-EM structure of yeast Mgm101 in the lock-washer apo state
ComponentsMitochondrial genome maintenance protein MGM101
KeywordsDNA BINDING PROTEIN / Single strand annealing protein / SSAP / annealase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWheat, C.T. / Bell, C.E.
Funding support United States, 1items
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, C.T. / Bell, C.E.
History
DepositionOct 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial genome maintenance protein MGM101
B: Mitochondrial genome maintenance protein MGM101
C: Mitochondrial genome maintenance protein MGM101
D: Mitochondrial genome maintenance protein MGM101
E: Mitochondrial genome maintenance protein MGM101
F: Mitochondrial genome maintenance protein MGM101
G: Mitochondrial genome maintenance protein MGM101
H: Mitochondrial genome maintenance protein MGM101
I: Mitochondrial genome maintenance protein MGM101
J: Mitochondrial genome maintenance protein MGM101
K: Mitochondrial genome maintenance protein MGM101
L: Mitochondrial genome maintenance protein MGM101
M: Mitochondrial genome maintenance protein MGM101
N: Mitochondrial genome maintenance protein MGM101
O: Mitochondrial genome maintenance protein MGM101
P: Mitochondrial genome maintenance protein MGM101
R: Mitochondrial genome maintenance protein MGM101
S: Mitochondrial genome maintenance protein MGM101


Theoretical massNumber of molelcules
Total (without water)513,44218
Polymers513,44218
Non-polymers00
Water00
1


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

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Components

#1: Protein
Mitochondrial genome maintenance protein MGM101


Mass: 28524.535 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MGM101, MGM9, YJR144W, J2181 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P32787
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: Cryo-EM structure of yeast Mgm101 in the lock-washer apo state
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.512 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 2.6 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2EPUimage acquisition
7UCSF ChimeraX1.9model fitting
9PHENIX1.21.2_5419model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 493000 / Symmetry type: POINT
RefinementHighest resolution: 2.96 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00326660
ELECTRON MICROSCOPYf_angle_d0.69835950
ELECTRON MICROSCOPYf_dihedral_angle_d4.0243514
ELECTRON MICROSCOPYf_chiral_restr0.0483834
ELECTRON MICROSCOPYf_plane_restr0.0064502

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