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- PDB-8fy3: Structure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex -

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Basic information

Entry
Database: PDB / ID: 8fy3
TitleStructure of NOT1:NOT10:NOT11 module of the human CCR4-NOT complex
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 10
  • CCR4-NOT transcription complex subunit 11
KeywordsRNA BINDING PROTEIN / mRNA degradation / gene expression
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / armadillo repeat domain binding / CCR4-NOT complex / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / 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 / mRNA catabolic process / nuclear estrogen receptor binding / P-body / negative regulation of translation / molecular adaptor activity / protein domain specific binding / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily / CCR4-NOT transcription complex subunit 1 ...CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 / CCR4-NOT transcription complex subunit 1, CAF1-binding domain / CCR4-NOT transcription complex subunit 1, TTP binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat / CCR4-NOT subunit 1, TTP binding domain superfamily / CCR4-NOT transcription complex subunit 1 / CCR4-Not complex component, Not1 / CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819 / CCR4-NOT transcription complex subunit 1 CAF1-binding domain / CCR4-NOT transcription complex subunit 1 TTP binding domain / CCR4-NOT transcription complex subunit 1 HEAT repeat / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsLea, S.M. / Deme, J.C. / Raisch, T. / Pekovic, F. / Valkov, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Commun Biol / Year: 2023
Title: Structure and assembly of the NOT10:11 module of the CCR4-NOT complex.
Authors: Yevgen Levdansky / Tobias Raisch / Justin C Deme / Filip Pekovic / Hans Elmlund / Susan M Lea / Eugene Valkov /
Abstract: NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT ...NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 1
B: CCR4-NOT transcription complex subunit 10
C: CCR4-NOT transcription complex subunit 11


Theoretical massNumber of molelcules
Total (without water)217,8703
Polymers217,8703
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein CCR4-NOT transcription complex subunit 1 / CCR4-associated factor 1 / Negative regulator of transcription subunit 1 homolog / NOT1H / hNOT1


Mass: 111576.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT1, CDC39, KIAA1007, NOT1, AD-005 / Production host: Escherichia coli (E. coli) / References: UniProt: A5YKK6
#2: Protein CCR4-NOT transcription complex subunit 10


Mass: 75931.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9A5
#3: Protein CCR4-NOT transcription complex subunit 11


Mass: 30362.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B3KNB0

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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: NOT1:NOT10:NOT11 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 250 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: dev_4788: / Classification: refinement
EM software
IDNameVersionCategory
1SIMPLE3particle selection
4SIMPLE3CTF correction
10cryoSPARC3.31initial Euler assignment
11cryoSPARC3.31final Euler assignment
12cryoSPARC3.31classification
13cryoSPARC3.313D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 387942 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039137
ELECTRON MICROSCOPYf_angle_d0.46912357
ELECTRON MICROSCOPYf_dihedral_angle_d11.5063383
ELECTRON MICROSCOPYf_chiral_restr0.0361393
ELECTRON MICROSCOPYf_plane_restr0.0041577

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