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- PDB-8bfi: human CNOT1-CNOT10-CNOT11 module -

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Basic information

Entry
Database: PDB / ID: 8bfi
Titlehuman CNOT1-CNOT10-CNOT11 module
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 10
  • CCR4-NOT transcription complex subunit 11
KeywordsRNA BINDING PROTEIN / N-Terminal module CCR4-NOT complex
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated post-transcriptional gene silencing ...positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / positive regulation of mRNA catabolic process / negative regulation of retinoic acid receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated post-transcriptional gene silencing / trophectodermal cell differentiation / 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 / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / regulation of translation / molecular adaptor activity / negative regulation of translation / protein domain specific binding / negative regulation of transcription by RNA polymerase II / extracellular space / RNA binding / nucleus / membrane / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / : / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-NOT transcription complex subunit 1, NOT1_connector / : / 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 10 / CCR4-NOT transcription complex subunit 11 / CCR4-NOT transcription complex subunit 11 / : / CCR4-NOT transcription complex subunit 1, N-terminal domain / CCR4-NOT transcription complex subunit 1, NOT1_connector / : / 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 repeat domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 10 / CCR4-NOT transcription complex subunit 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsBasquin, J. / Ozgur, S. / Conti, E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)EXORICOEuropean Union
CitationJournal: Cell Rep / Year: 2023
Title: The human CNOT1-CNOT10-CNOT11 complex forms a structural platform for protein-protein interactions.
Authors: Mauxion, F. / Basquin, J. / Ozgur, S. / Rame, M. / Albrecht, J. / Schafer, I. / Seraphin, B. / Conti, E.
History
DepositionOct 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)218,3003
Polymers218,3003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17880 Å2
ΔGint-108 kcal/mol
Surface area74090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.760, 110.640, 128.580
Angle α, β, γ (deg.)90.000, 103.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 88423.750 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: 79251.742 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: 50624.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT11, C2orf29, C40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKZ1
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 5% (w/v) PEG 3500, 2% (v/v) isopropanol, 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→45.77 Å / Num. obs: 89839 / % possible obs: 99.96 % / Redundancy: 68.3 % / Biso Wilson estimate: 85.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.3212 / Net I/σ(I): 22.31
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 4548 / CC1/2: 0.435

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→45.77 Å / SU ML: 0.4862 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 31.0387
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2827 4497 5.01 %
Rwork0.262 85342 -
obs0.2631 89839 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 106.26 Å2
Refinement stepCycle: LAST / Resolution: 3→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11891 0 0 0 11891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002412126
X-RAY DIFFRACTIONf_angle_d0.627216483
X-RAY DIFFRACTIONf_chiral_restr0.03811929
X-RAY DIFFRACTIONf_plane_restr0.00442130
X-RAY DIFFRACTIONf_dihedral_angle_d5.80581664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.37491480.40762789X-RAY DIFFRACTION99.59
3.03-3.070.37941470.38142848X-RAY DIFFRACTION99.57
3.07-3.110.35561510.33452865X-RAY DIFFRACTION100
3.11-3.150.36561490.3272821X-RAY DIFFRACTION100
3.15-3.190.33931530.3022874X-RAY DIFFRACTION99.97
3.19-3.230.35491510.30272896X-RAY DIFFRACTION99.97
3.23-3.280.3441400.29022744X-RAY DIFFRACTION99.97
3.28-3.330.31681530.3112920X-RAY DIFFRACTION100
3.33-3.380.34441490.3072845X-RAY DIFFRACTION99.97
3.38-3.430.33391510.31222819X-RAY DIFFRACTION100
3.43-3.490.37551490.29992866X-RAY DIFFRACTION99.97
3.49-3.560.32271520.27372858X-RAY DIFFRACTION100
3.56-3.630.25361440.27282792X-RAY DIFFRACTION100
3.63-3.70.27041510.25052845X-RAY DIFFRACTION100
3.7-3.780.31741510.26062859X-RAY DIFFRACTION100
3.78-3.870.30061530.26612881X-RAY DIFFRACTION100
3.87-3.960.29981500.25092842X-RAY DIFFRACTION100
3.96-4.070.28341520.2672813X-RAY DIFFRACTION100
4.07-4.190.30581530.27252876X-RAY DIFFRACTION99.97
4.19-4.330.25611510.23872824X-RAY DIFFRACTION100
4.33-4.480.23171460.23982856X-RAY DIFFRACTION100
4.48-4.660.26991530.24122853X-RAY DIFFRACTION100
4.66-4.870.26161460.24022826X-RAY DIFFRACTION100
4.87-5.130.2391470.25352857X-RAY DIFFRACTION100
5.13-5.450.35871500.27352857X-RAY DIFFRACTION100
5.45-5.870.33531520.29482836X-RAY DIFFRACTION100
5.87-6.460.28241480.3062862X-RAY DIFFRACTION100
6.46-7.390.27991520.25492826X-RAY DIFFRACTION100
7.39-9.290.22371530.21352877X-RAY DIFFRACTION100
9.3-45.770.22651520.21942815X-RAY DIFFRACTION99.73

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