9E7T | pdb_00009e7t

Cryo-EM structure of NOT1:NOT7:PieF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay.

Levdansky, Y.Deme, J.C.Turner, D.J.Piczak, C.T.Pekovic, F.Valkov, A.L.Tarasov, S.G.Lea, S.M.Valkov, E.

(2025) Nat Commun 16: 6452-6452

  • DOI: https://doi.org/10.1038/s41467-025-61194-2
  • Primary Citation of Related Structures:  
    9E7T, 9E7U

  • PubMed Abstract: 

    Legionella pneumophila, an intracellular bacterial pathogen, injects effector proteins into host cells to manipulate cellular processes and promote its survival and proliferation. Here, we reveal a unique mechanism by which the Legionella effector PieF perturbs host mRNA decay by targeting the human CCR4-NOT deadenylase complex. High-resolution cryo-electron microscopy structures and biochemical analyses reveal that PieF binds with nanomolar affinity to the NOT7 and NOT8 catalytic subunits of CCR4-NOT, obstructing RNA access and displacing a catalytic Mg²⁺ ion from the active site. Additionally, PieF prevents NOT7/8 from associating with their partner deadenylases NOT6/6L, inhibiting the assembly of a functional deadenylase complex. Consequently, PieF robustly blocks mRNA poly(A) tail shortening and degradation with striking potency and selectivity for NOT7/8. This inhibition of deadenylation by PieF impedes cell cycle progression in human cells, revealing a novel bacterial strategy to modulate host gene expression.


  • Organizational Affiliation
    • National Cancer Institute, National Institutes of Health, Frederick, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dot/Icm T4SS effector PieF150Legionella pneumophilaMutation(s): 0 
Gene Names: pieFJBJ86_12865
UniProt
Find proteins for Q5ZU36 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZU36 
Go to UniProtKB:  Q5ZU36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZU36
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CCR4-NOT transcription complex subunit 1254Homo sapiensMutation(s): 0 
Gene Names: CNOT1CDC39KIAA1007NOT1AD-005
UniProt & NIH Common Fund Data Resources
Find proteins for A5YKK6 (Homo sapiens)
Explore A5YKK6 
Go to UniProtKB:  A5YKK6
PHAROS:  A5YKK6
GTEx:  ENSG00000125107 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5YKK6
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SDH7p Mitochondrial protein involved in assembly of succinate dehydrogenase,CCR4-NOT transcription complex subunit 7411Homo sapiensMutation(s): 0 
Gene Names: KO01_01272CNOT7CAF1
EC: 3.1.13.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIV1 (Homo sapiens)
Explore Q9UIV1 
Go to UniProtKB:  Q9UIV1
PHAROS:  Q9UIV1
GTEx:  ENSG00000198791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIV1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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 StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release