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- PDB-9c3i: Rebuilt CNOT3/tRNA-LEU structure -

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Basic information

Entry
Database: PDB / ID: 9c3i
TitleRebuilt CNOT3/tRNA-LEU structure
Components
  • CCR4-NOT transcription complex subunit 3
  • tRNA Leu, UAA-1-1
KeywordsTRANSCRIPTION / mRNA degradation / CCR4-NOT complex / tRNA
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / P-body ...CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / P-body / regulation of translation / positive regulation of cold-induced thermogenesis / regulation of DNA-templated transcription / nucleus / cytosol
Similarity search - Function
CCR4-Not complex component, Not N-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex, subunit 3/ 5 / Not1 N-terminal domain, CCR4-Not complex component / NOT2/NOT3/NOT5 C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5
Similarity search - Domain/homology
RNA / RNA (> 10) / CCR4-NOT transcription complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsErzberger, J.P. / Cruz, V.E.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA282036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM135617-01 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220309 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150074 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
Welch FoundationI-1961 United States
Welch FoundationI-1897 United States
CitationJournal: Science / Year: 2024
Title: Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes.
Authors: Xiaoqiang Zhu / Victor Emmanuel Cruz / He Zhang / Jan P Erzberger / Joshua T Mendell /
Abstract: The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. ...The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. Cryo-electron microscopy and transfer RNA (tRNA) mutagenesis demonstrated that the D-arms of select arginine tRNAs interact with CNOT3 and promote its recruitment whereas other tRNA D-arms sterically clash with CNOT3. These effects link codon content to mRNA stability. Thus, in addition to their canonical decoding function, tRNAs directly engage regulatory complexes during translation, a mechanism we term P-site tRNA-mediated mRNA decay.
History
DepositionJun 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Remark 0THIS ENTRY 9C3I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 8BHF, DETERMINED BY ...THIS ENTRY 9C3I REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 8BHF, DETERMINED BY Absmeier, E., Chandrasekaran, V., O'Reilly, F.J., Stowell, J.A.W., Rappsilber, J., Passmore, L.A.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: CCR4-NOT transcription complex subunit 3
A: tRNA Leu, UAA-1-1


Theoretical massNumber of molelcules
Total (without water)91,8562
Polymers91,8562
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein CCR4-NOT transcription complex subunit 3 / CCR4-associated factor 3 / Leukocyte receptor cluster member 2


Mass: 64125.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT3, KIAA0691, LENG2, NOT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O75175
#2: RNA chain tRNA Leu, UAA-1-1


Mass: 27730.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CNOT3/tRNA-Leu / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 100000 / Symmetry type: POINT

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