7ZR1 | pdb_00007zr1

Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite structure)

PDB DOI: https://doi.org/10.2210/pdb7ZR1/pdb
EM Map EMD-14881: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Thermochaetoides thermophila DSM 1495, Thermochaetoides thermophila
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-05-03 Released: 2023-01-11
Deposition Author(s): Bartho, J.D., Rotheneder, M., Stakyte, K., Lammens, K., Hopfner, K.P.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cryo-EM structure of the Mre11-Rad50-Nbs1 complex reveals the molecular mechanism of scaffolding functions.

Rotheneder, M., Stakyte, K., van de Logt, E., Bartho, J.D., Lammens, K., Fan, Y., Alt, A., Kessler, B., Jung, C., Roos, W.P., Steigenberger, B., Hopfner, K.P.

(2023) Mol Cell 83: 167-185.e9

PubMed: 36577401 Search on PubMed
DOI: https://doi.org/10.1016/j.molcel.2022.12.003
Primary Citation Related Structures:
7ZQY, 7ZR1, 8BAH

PubMed 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 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.

Organizational Affiliation

Gene Center, Department of Biochemistry, Ludwig Maximilians Universität, Munich, Germany.

Macromolecule Content

Total Structure Weight: 577.83 kDa
Atom Count: 21,793
Modeled Residue Count: 2,686
Deposited Residue Count: 5,044
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-strand break repair protein	A, B	730	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0007600 EC: 3.1
UniProt
Find proteins for G0RYR3 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0RYR3 Go to UniProtKB: G0RYR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0RYR3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH domain-containing protein	C, D	1,315	Thermochaetoides thermophila	Mutation(s): 0 Gene Names: CTHT_0073630 EC: 3.6
UniProt
Find proteins for G0SHW7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SHW7 Go to UniProtKB: G0SHW7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SHW7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FHA domain-containing protein	E	954	Thermochaetoides thermophila DSM 1495	Mutation(s): 0 Gene Names: CTHT_0047880
UniProt
Find proteins for G0SAV1 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0SAV1 Go to UniProtKB: G0SAV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0SAV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGS (Subject of Investigation/LOI) Query on AGS Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C]	K [auth C], M [auth D]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C₁₀ H₁₆ N₅ O₁₂ P₃ S NLTUCYMLOPLUHL-KQYNXXCUSA-N		Interactions Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain K [auth C] Focus chain M [auth D]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth B], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C]	J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain J [auth C] Focus chain L [auth D]