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- PDB-9bi5: Apo form Mre11-Rad50 complex -

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Basic information

Entry
Database: PDB / ID: 9bi5
TitleApo form Mre11-Rad50 complex
Components
  • DNA repair protein RAD50
  • Double-strand break repair protein MRE11
KeywordsDNA BINDING PROTEIN / MRN / Mre11 / Rad50 / Nbs1 / DNA binding / DNA damage / DNA repair
Function / homology
Function and homology information


DNA double-strand break processing involved in repair via synthesis-dependent strand annealing / nucleoside monophosphate phosphorylation / Cytosolic sensors of pathogen-associated DNA / meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / ascospore formation ...DNA double-strand break processing involved in repair via synthesis-dependent strand annealing / nucleoside monophosphate phosphorylation / Cytosolic sensors of pathogen-associated DNA / meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / ascospore formation / R-loop processing / Hydrolases; Acting on acid anhydrides / single-stranded DNA endodeoxyribonuclease activity / chromosome organization involved in meiotic cell cycle / AMP kinase activity / homologous chromosome pairing at meiosis / maintenance of DNA trinucleotide repeats / double-stranded telomeric DNA binding / G-quadruplex DNA binding / 3'-5'-DNA exonuclease activity / DNA double-strand break processing / single-stranded telomeric DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / telomere maintenance via recombination / double-strand break repair via break-induced replication / reciprocal meiotic recombination / mitotic intra-S DNA damage checkpoint signaling / telomeric DNA binding / mitotic G2 DNA damage checkpoint signaling / telomere maintenance via telomerase / 3'-5' exonuclease activity / telomere maintenance / condensed nuclear chromosome / DNA endonuclease activity / meiotic cell cycle / double-strand break repair via homologous recombination / base-excision repair / double-strand break repair via nonhomologous end joining / double-strand break repair / manganese ion binding / site of double-strand break / double-stranded DNA binding / endonuclease activity / molecular adaptor activity / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA repair / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
DNA repair protein Rad50, eukaryotes / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Mre11 nuclease, N-terminal metallophosphatase domain ...DNA repair protein Rad50, eukaryotes / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Mre11 nuclease, N-terminal metallophosphatase domain / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA repair protein RAD50 / Double-strand break repair protein MRE11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYu, Y. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136278 United States
CitationJournal: To Be Published
Title: cryo EM structure of Apo form Mre11-Rad50 complex
Authors: Yu, Y. / Patel, D.J.
History
DepositionApr 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 6, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Data processing / Category: em_3d_reconstruction / em_admin
Item: _em_3d_reconstruction.resolution / _em_admin.last_update
Revision 1.1Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_3d_reconstruction / em_admin / Data content type: EM metadata / EM metadata
Item: _em_3d_reconstruction.resolution / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA repair protein RAD50
A: Double-strand break repair protein MRE11
C: DNA repair protein RAD50
B: Double-strand break repair protein MRE11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,04410
Polymers464,8104
Non-polymers1,2346
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DNA repair protein RAD50 / 153 kDa protein


Mass: 152797.688 Da / Num. of mol.: 2 / Mutation: E1235Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAD50, YNL250W, N0872 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P12753, Hydrolases; Acting on acid anhydrides
#2: Protein Double-strand break repair protein MRE11


Mass: 79607.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MRE11, YMR224C, YM9959.06C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32829
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Apo form yeast Mre11-Rad50 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.46 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Details: 50 mM Hepes, pH 7.5, 200 mM NaCl, 2 mM DTT, 2% Glycerol, 0.025% (w/v) CHAPSO (3-([3-Cholamidopropyl]dimethylammonio)-2-hydroxy-1-propanesulfonate)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.22 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 232521 / Symmetry type: POINT

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