9Q9K | pdb_00009q9k

Cryo-EM structure of human Mre11-Rad50 (MR) complex bound to DNA and telomeric factor TRF2 fragment (438-542)

PDB DOI: https://doi.org/10.2210/pdb9Q9K/pdb
NAKB: 9Q9K
EM Map EMD-52962: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-02-26 Released: 2025-10-01
Deposition Author(s): Cui, H.J., Lammens, K., Hopfner, K.P., Fan, Y.L., Kuybu, F.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Structural basis for DNA break sensing by human MRE11-RAD50-NBS1 and its regulation by telomeric factor TRF2.

Fan, Y., Kuybu, F., Cui, H., Lammens, K., Chen, J.X., Kugler, M., Jung, C., Hopfner, K.P.

(2025) Nat Commun 16: 8320-8320

PubMed: 40968163 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-64082-x
Primary Citation Related Structures:
9Q9H, 9Q9I, 9Q9J, 9Q9K, 9Q9M

PubMed Abstract:
The MRE11-RAD50-NBS1 (MRN) complex is a central, multifunctional factor in the detection, signaling and nucleolytic processing of DNA double-strand breaks (DSBs). To clarify how human MRN binds generic and telomeric DNA ends and can separate DNA end sensing from nuclease activities, we determined cryo-electron microscopy (cryo-EM) structures of human MRN bound to DNA and to DNA and the telomere protection factor TRF2. MRN senses DSBs through a tight clamp-like sensing state with closed coiled-coil domains, but auto-inhibited MRE11 nuclease. NBS1 wraps around the MRE11 dimer, with NBS1's ATM recruitment motif sequestered by binding to the regulatory RAD50 S site, necessitating a switch in the NBS1 C helix for ATM activation. At telomeric DNA, TRF2 blocks the second S site via the iDDR motif to prevent nuclease and ATM activation. Our results provide a structural framework for DNA sensing via a gating mechanism and separation of sensing, signaling and processing activities of mammalian MRN.

Organizational Affiliation

Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377, Munich, Germany.

Macromolecule Content

Total Structure Weight: 542.91 kDa
Atom Count: 16,910
Modeled Residue Count: 1,988
Deposited Residue Count: 4,460
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Telomeric repeat-binding factor 2	A [auth J], B [auth K]	116	Homo sapiens	Mutation(s): 0 Gene Names: TERF2, TRBF2, TRF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15554 (Homo sapiens) Explore Q15554 Go to UniProtKB: Q15554
PHAROS: Q15554 GTEx: ENSG00000132604
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15554
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD50	E [auth A], F [auth B]	1,312	Homo sapiens	Mutation(s): 0 Gene Names: RAD50 EC: 3.6
UniProt & NIH Common Fund Data Resources
Find proteins for Q92878 (Homo sapiens) Explore Q92878 Go to UniProtKB: Q92878
PHAROS: Q92878 GTEx: ENSG00000113522
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92878
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Double-strand break repair protein MRE11	G [auth D], H [auth E]	738	Homo sapiens	Mutation(s): 0 Gene Names: MRE11, HNGS1, MRE11A EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49959 (Homo sapiens) Explore P49959 Go to UniProtKB: P49959
PHAROS: P49959 GTEx: ENSG00000020922
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49959
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 2
DNA (64-MER)	C [auth P]	64	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (64-MER)	D [auth T]	64	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A], L [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth B]
BEF (Subject of Investigation/LOI) Query on BEF Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A]	K [auth A], N [auth B]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain K [auth A] Focus chain N [auth B]
MN (Subject of Investigation/LOI) Query on MN Download:Ideal Coordinates CCD File SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D]	O [auth D], P [auth D], Q [auth E], R [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Interactions & Density Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	J [auth A], M [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth B]