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Open data
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Basic information
Entry | Database: PDB / ID: 8bah | |||||||||||||||
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Title | Human Mre11-Nbs1 complex | |||||||||||||||
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![]() | HYDROLASE / DNA repair / complex | |||||||||||||||
Function / homology | ![]() telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / blastocyst growth / telomere maintenance in response to DNA damage / negative regulation of telomere capping / protection from non-homologous end joining at telomere ...telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / mitochondrial double-strand break repair via homologous recombination / Mre11 complex / negative regulation of double-strand break repair via nonhomologous end joining / blastocyst growth / telomere maintenance in response to DNA damage / negative regulation of telomere capping / protection from non-homologous end joining at telomere / meiotic DNA double-strand break formation / Sensing of DNA Double Strand Breaks / BRCA1-C complex / regulation of mitotic recombination / R-loop processing / phosphorylation-dependent protein binding / t-circle formation / chromatin-protein adaptor activity / homologous chromosome pairing at meiosis / DNA strand resection involved in replication fork processing / DNA double-strand break processing / nuclease activity / single-stranded DNA endodeoxyribonuclease activity / homologous recombination / nuclear inclusion body / positive regulation of telomere maintenance / Cytosolic sensors of pathogen-associated DNA / isotype switching / protein localization to site of double-strand break / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / IRF3-mediated induction of type I IFN / mitotic G2/M transition checkpoint / positive regulation of kinase activity / reciprocal meiotic recombination / sister chromatid cohesion / mitotic intra-S DNA damage checkpoint signaling / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / regulation of DNA-templated DNA replication initiation / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / 3'-5'-DNA exonuclease activity / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / double-strand break repair via alternative nonhomologous end joining / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / protein K63-linked ubiquitination / neuromuscular process controlling balance / positive regulation of double-strand break repair via homologous recombination / DNA damage response, signal transduction by p53 class mediator / telomere maintenance via telomerase / neuroblast proliferation / positive regulation of protein autophosphorylation / 3'-5' exonuclease activity / telomere maintenance / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / meiotic cell cycle / DNA endonuclease activity / replication fork / DNA damage checkpoint signaling / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / DNA Damage/Telomere Stress Induced Senescence / PML body / Meiotic recombination / double-strand break repair via nonhomologous end joining / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / manganese ion binding / Processing of DNA double-strand break ends / histone binding / double-stranded DNA binding / DNA recombination / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / regulation of cell cycle / cadherin binding / DNA repair / DNA damage response / nucleolus / negative regulation of apoptotic process / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.13 Å | |||||||||||||||
![]() | Bartho, J.D. / Rotheneder, M. / Stakyte, K. / Lammens, K. / Hopfner, K.P. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.3 KB | Display | ![]() |
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PDB format | ![]() | 244 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 50.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15948MC ![]() 7zqyC ![]() 7zr1C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 84008.633 Da / Num. of mol.: 2 / Mutation: H129N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P49959, Hydrolases; Acting on ester bonds #2: Protein | | Mass: 85073.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-MN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human Mre11-Nbs1 complex / Type: COMPLEX Details: Human Mre11-dimer with Nbs1 C-terminal chain bound. Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7 Details: 20 mM HEPES (pH 7.0), 140 mM NaCl, 5 mM MgCl2, 1 mM MnCl2, 0.020 mM ZnCl2, 0.2 mM TCEP, 2 mM ATPgS, plus 0.05 percent beta-OG | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.29 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 13000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 43 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 11325 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282838 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
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