9BI4

cryo EM structure of dsDNA bound Mre11-Rad50 complex

PDB DOI: https://doi.org/10.2210/pdb9BI4/pdb
EM Map EMD-44558: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Saccharomyces cerevisiae, synthetic construct
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2024-04-22 Released: 2025-01-15
Deposition Author(s): Yu, Y., Patel, D.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure guided functional analysis of the S. cerevisiae Mre11 complex.

Petrini, J., Hohl, M., Yu, Y., Kuryavyi, V., Patel, D.

(2024) Res Sq

PubMed: 39711558 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.21203/rs.3.rs-5390974/v1
Primary Citation of Related Structures:
9BI4

PubMed Abstract:
The Mre11 complex comprises Mre11, Rad50 and Nbs1 (Xrs2 in S. cerevisiae ). The core components, Mre11 and Rad50 are highly conserved, with readily identifiable orthologs in all clades of life, whereas Nbs1/Xrs2 are present only in eukaryotes. In eukaryotes, the complex is integral to the DNA damage response, acting in DNA double strand break (DSB) detection and repair, and the activation of DNA damage signaling. We present here a 3.2 Å cryo-EM structure of the S. cerevisiae Mre11-Rad50 complex with bound dsDNA. The structure provided a foundation for detailed mutational analyses regarding homo and heterotypic protein interfaces, as well as DNA binding properties of Rad50. We define several conserved residues in Rad50 and Mre11 that are critical to complex assembly as well as for DNA binding. In addition, the data reveal that the Rad50 coiled coil domain influences ATP hydrolysis over long distances.

Organizational Affiliation

Memorial Sloan Kettering Cancer Center.

Macromolecule Content

Total Structure Weight: 517.25 kDa
Atom Count: 15,869
Modelled Residue Count: 1,925
Deposited Residue Count: 4,202
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD50	A [auth C], B [auth D]	1,312	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: RAD50, YNL250W, N0872 EC: 3.6
UniProt
Find proteins for P12753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12753 Go to UniProtKB: P12753
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12753
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-strand break repair protein MRE11	C [auth B], E [auth A]	706	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: MRE11, YMR224C, YM9959.06C EC: 3.1
UniProt
Find proteins for P32829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32829 Go to UniProtKB: P32829
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32829
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
one strand of dsDNA	D [auth E]	83	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
second strand of dsDNA	F	83	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain I [auth D] MOL2 format, chain G [auth C] MOL2 format, chain I [auth D] mmCIF format, chain G [auth C] mmCIF format, chain I [auth D]	G [auth C], I [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth C] Focus chain I [auth D] Interactions & Density Focus chain G [auth C] Focus chain I [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A]	K [auth B], L [auth B], M [auth A], N [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth A] Focus chain N [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain J [auth D] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D]	H [auth C], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain J [auth D] Interactions & Density Focus chain H [auth C] Focus chain J [auth D]