7SID

Human ATM Dimer Bound to Nbs1

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-10-13 Released: 2022-02-02 
  • Deposition Author(s): Warren, C., Pavletich, N.P.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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 of the human ATM kinase and mechanism of Nbs1 binding.

Warren, C.Pavletich, N.P.

(2022) Elife 11

  • DOI: https://doi.org/10.7554/eLife.74218
  • Primary Citation of Related Structures:  
    7SIC, 7SID

  • PubMed Abstract: 

    DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, which belongs to the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family. In response to DSBs, ATM is activated by the MRN (Mre11-Rad50-Nbs1) protein complex through a poorly understood process that also requires double-stranded DNA. Previous studies indicate that the FxF/Y motif of Nbs1 directly binds to ATM, and is required to retain active ATM at sites of DNA damage. Here, we report the 2.5 Å resolution cryo-EM structures of human ATM and its complex with the Nbs1 FxF/Y motif. In keeping with previous structures of ATM and its yeast homolog Tel1, the dimeric human ATM kinase adopts a symmetric, butterfly-shaped structure. The conformation of the ATM kinase domain is most similar to the inactive states of other PIKKs, suggesting that activation may involve an analogous realigning of the N and C lobes along with relieving the blockage of the substrate-binding site. We also show that the Nbs1 FxF/Y motif binds to a conserved hydrophobic cleft within the Spiral domain of ATM, suggesting an allosteric mechanism of activation. We evaluate the importance of these structural findings with mutagenesis and biochemical assays.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine-protein kinase ATM
A, C
3,056Homo sapiensMutation(s): 0 
Gene Names: ATM
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13315 (Homo sapiens)
Explore Q13315 
Go to UniProtKB:  Q13315
PHAROS:  Q13315
GTEx:  ENSG00000149311 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13315
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nibrin
B, D
28Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60934 (Homo sapiens)
Explore O60934 
Go to UniProtKB:  O60934
PHAROS:  O60934
GTEx:  ENSG00000104320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60934
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5F32CA247320
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesCA008748

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release