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Open data
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Basic information
Entry | Database: PDB / ID: 9e7u | ||||||
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Title | Cryo-EM structure of NOT1:NOT8:PieF | ||||||
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![]() | GENE REGULATION / PieF / mRNA decay / deadenylation / CCR4-NOT / host-pathogen interactions | ||||||
Function / homology | ![]() positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / regulation of stem cell population maintenance / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins ...positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / regulation of stem cell population maintenance / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / nuclear-transcribed mRNA poly(A) tail shortening / septin ring / SUMOylation of DNA damage response and repair proteins / negative regulation of intracellular estrogen receptor signaling pathway / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / M-decay: degradation of maternal mRNAs by maternally stored factors / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / peroxisomal membrane / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / nuclear estrogen receptor binding / P-body / protein tag activity / regulation of translation / 3'-5'-RNA exonuclease activity / molecular adaptor activity / negative regulation of translation / protein domain specific binding / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
![]() | Levdansky, E. / Deme, J. / Lea, S.M. / Valkov, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Intracellular pathogen effector reprograms host gene expression by inhibiting mRNA decay. Authors: Yevgen Levdansky / Justin C Deme / David J Turner / Claire T Piczak / Filip Pekovic / Anna L Valkov / Sergey G Tarasov / Susan M Lea / Eugene Valkov / ![]() 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 ...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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.5 KB | Display | ![]() |
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PDB format | ![]() | 91.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 54.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 47690MC ![]() 9e7tC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 47754.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q12306, UniProt: Q9UFF9, poly(A)-specific ribonuclease |
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#2: Protein | Mass: 16568.549 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 29237.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: NOT1:NOT8:PieF / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 52.4 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
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Processing
EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200675 / Symmetry type: POINT | ||||||||||||||||||||||||
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