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- PDB-4ct6: CNOT9-CNOT1 complex -

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Basic information

Entry
Database: PDB / ID: 4ct6
TitleCNOT9-CNOT1 complex
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
KeywordsTRANSCRIPTION
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 / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway ...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 / sex differentiation / 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 / epidermal growth factor receptor binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of peptidyl-serine phosphorylation / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / molecular adaptor activity / transcription coactivator activity / negative regulation of translation / protein domain specific binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / extracellular space / RNA binding / nucleus / membrane / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / : / 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 9 / Cell differentiation family, Rcd1-like / : / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsBasquin, J. / Ozgur, S. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression.
Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W.
History
DepositionMar 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)58,1342
Polymers58,1342
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-26.2 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.670, 66.142, 72.436
Angle α, β, γ (deg.)90.00, 100.35, 90.00
Int Tables number5
Space group name H-MC121

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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 / ...CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1 / CNOT1-DUF-DOMAIN


Mass: 27470.666 Da / Num. of mol.: 1 / Fragment: DUF DOMAIN, RESIDUES 1352-1594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_GST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: A5YKK6
#2: Protein CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG / RCD-1 / CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 9 / CNOT9


Mass: 30663.658 Da / Num. of mol.: 1 / Fragment: RESIDUES 18-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: Q92600
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

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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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6
Details: 20% PEG 3550, 200 MM AMMONIUM SULFATE, 50 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2→47.9 Å / Num. obs: 41743 / % possible obs: 98.9 % / Observed criterion σ(I): 4.2 / Redundancy: 4.6 % / Biso Wilson estimate: 39.31 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.2 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FV2

2fv2


Resolution: 2.099→47.895 Å / SU ML: 0.27 / σ(F): 1.3 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 4061 5 %
Rwork0.1941 --
obs0.1962 41716 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→47.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 0 417 4378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094038
X-RAY DIFFRACTIONf_angle_d1.1685483
X-RAY DIFFRACTIONf_dihedral_angle_d13.9811522
X-RAY DIFFRACTIONf_chiral_restr0.045645
X-RAY DIFFRACTIONf_plane_restr0.007704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0986-2.12330.37491210.34882301X-RAY DIFFRACTION85
2.1233-2.14920.40461380.32032638X-RAY DIFFRACTION99
2.1492-2.17640.32291390.29192633X-RAY DIFFRACTION99
2.1764-2.2050.30891420.2772720X-RAY DIFFRACTION99
2.205-2.23520.35781380.26722592X-RAY DIFFRACTION99
2.2352-2.26720.27581460.27062716X-RAY DIFFRACTION99
2.2672-2.3010.32641400.2562640X-RAY DIFFRACTION99
2.301-2.33690.2511410.24162694X-RAY DIFFRACTION99
2.3369-2.37530.29911380.22982627X-RAY DIFFRACTION99
2.3753-2.41620.2871450.22152697X-RAY DIFFRACTION99
2.4162-2.46020.29721430.21842703X-RAY DIFFRACTION99
2.4602-2.50750.27441390.20232608X-RAY DIFFRACTION99
2.5075-2.55860.21351360.21052662X-RAY DIFFRACTION100
2.5586-2.61430.25731450.20462705X-RAY DIFFRACTION99
2.6143-2.67510.23591430.2012667X-RAY DIFFRACTION100
2.6751-2.7420.20881420.20412658X-RAY DIFFRACTION99
2.742-2.81610.27021380.20722663X-RAY DIFFRACTION99
2.8161-2.8990.28681440.20572701X-RAY DIFFRACTION99
2.899-2.99250.26081410.2042674X-RAY DIFFRACTION99
2.9925-3.09950.25921360.21562638X-RAY DIFFRACTION99
3.0995-3.22350.2691400.19952679X-RAY DIFFRACTION99
3.2235-3.37020.18831410.20752669X-RAY DIFFRACTION99
3.3702-3.54780.25471410.17642618X-RAY DIFFRACTION99
3.5478-3.770.18811440.1812671X-RAY DIFFRACTION98
3.77-4.0610.23491400.17532653X-RAY DIFFRACTION98
4.061-4.46940.22521410.15362660X-RAY DIFFRACTION99
4.4694-5.11550.22461390.17212651X-RAY DIFFRACTION99
5.1155-6.44250.24461430.22662X-RAY DIFFRACTION99
6.4425-47.90760.15821370.15292647X-RAY DIFFRACTION98

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