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- PDB-7zr1: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (... -

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Basic information

Entry
Database: PDB / ID: 7zr1
TitleChaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)
Components
  • DH domain-containing protein
  • Double-strand break repair protein
  • FHA domain-containing protein
KeywordsHYDROLASE / DNA repair / complex / ATPase / coiled-coils
Function / homology
Function and homology information


mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / Hydrolases; Acting on acid anhydrides / single-stranded DNA endodeoxyribonuclease activity / chromosome organization involved in meiotic cell cycle / G-quadruplex DNA binding / 3'-5'-DNA exonuclease activity / double-stranded telomeric DNA binding / single-stranded telomeric DNA binding ...mitochondrial double-strand break repair via homologous recombination / Mre11 complex / meiotic DNA double-strand break formation / Hydrolases; Acting on acid anhydrides / single-stranded DNA endodeoxyribonuclease activity / chromosome organization involved in meiotic cell cycle / G-quadruplex DNA binding / 3'-5'-DNA exonuclease activity / double-stranded telomeric DNA binding / single-stranded telomeric DNA binding / telomere maintenance via recombination / mitotic intra-S DNA damage checkpoint signaling / mitotic G2 DNA damage checkpoint signaling / telomere maintenance via telomerase / telomere maintenance / guanyl-nucleotide exchange factor activity / condensed nuclear chromosome / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / manganese ion binding / chromosome / site of double-strand break / double-stranded DNA binding / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / ATP hydrolysis activity / metal ion binding
Similarity search - Function
Mre11, capping domain / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / DNA repair protein Rad50, eukaryotes / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain ...Mre11, capping domain / Nibrin, second BRCT domain / Nibrin, second BRCT domain superfamily / Second BRCT domain on Nijmegen syndrome breakage protein / DNA repair protein Rad50, eukaryotes / Nibrin-related / DNA double-strand break repair protein Mre11 / Mre11, DNA-binding / Mre11, capping domain / Mre11 DNA-binding presumed domain / Mre11 DNA-binding presumed domain / Mre11 nuclease, N-terminal metallophosphatase domain / SbcC/RAD50-like, Walker B motif / Rad50/SbcC-type AAA domain / AAA domain / Translation Initiation Factor IF3 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / Metallo-dependent phosphatases / FHA domain / Purple Acid Phosphatase; chain A, domain 2 / Forkhead-associated (FHA) domain / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / SMAD/FHA domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / BRCT domain superfamily / 4-Layer Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / : / Double-strand break repair protein MRE11 / DNA repair and telomere maintenance protein NBS1 / DNA repair protein RAD50
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsBartho, J.D. / Rotheneder, M. / Stakyte, K. / Lammens, K. / Hopfner, K.P.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1361 Germany
German Research Foundation (DFG)SFB1361 Germany
German Research Foundation (DFG)GRK1721 Germany
CitationJournal: Mol Cell / Year: 2023
Title: Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions.
Authors: Matthias Rotheneder / Kristina Stakyte / Erik van de Logt / Joseph D Bartho / Katja Lammens / Yilan Fan / Aaron Alt / Brigitte Kessler / Christophe Jung / Wynand P Roos / Barbara ...Authors: Matthias Rotheneder / Kristina Stakyte / Erik van de Logt / Joseph D Bartho / Katja Lammens / Yilan Fan / Aaron Alt / Brigitte Kessler / Christophe Jung / Wynand P Roos / Barbara Steigenberger / Karl-Peter Hopfner /
Abstract: The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as ...The DNA double-strand break repair complex Mre11-Rad50-Nbs1 (MRN) detects and nucleolytically processes DNA ends, activates the ATM kinase, and tethers DNA at break sites. How MRN can act both as nuclease and scaffold protein is not well understood. The cryo-EM structure of MRN from Chaetomium thermophilum reveals a 2:2:1 complex with a single Nbs1 wrapping around the autoinhibited Mre11 nuclease dimer. MRN has two DNA-binding modes, one ATP-dependent mode for loading onto DNA ends and one ATP-independent mode through Mre11's C terminus, suggesting how it may interact with DSBs and intact DNA. MRNs two 60-nm-long coiled-coil domains form a linear rod structure, the apex of which is assembled by the two joined zinc-hook motifs. Apices from two MRN complexes can further dimerize, forming 120-nm spanning MRN-MRN structures. Our results illustrate the architecture of MRN and suggest how it mechanistically integrates catalytic and tethering functions.
History
DepositionMay 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Double-strand break repair protein
B: Double-strand break repair protein
C: DH domain-containing protein
D: DH domain-containing protein
E: FHA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,82813
Polymers576,5135
Non-polymers1,3158
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25280 Å2
ΔGint-149 kcal/mol
Surface area135190 Å2
MethodPISA

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Components

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Protein , 3 types, 5 molecules ABCDE

#1: Protein Double-strand break repair protein


Mass: 83036.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0007600 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0RYR3
#2: Protein DH domain-containing protein


Mass: 152229.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0073630 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0SHW7
#3: Protein FHA domain-containing protein


Mass: 105980.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0047880 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0SAV1

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Non-polymers , 3 types, 8 molecules

#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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM

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Details

Has ligand of interestY

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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: Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.6
SpecimenConc.: 0.27 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: EPU / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288443 / Symmetry type: POINT

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