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- PDB-7voi: Structure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex -

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Basic information

Entry
Database: PDB / ID: 7voi
TitleStructure of the human CNOT1(MIF4G)-CNOT6L-CNOT7 complex
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 6-like
  • CCR4-NOT transcription complex subunit 7
KeywordsHYDROLASE / CCR4-NOT complex mRNA degradation / RNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / regulation of tyrosine phosphorylation of STAT protein / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / regulation of stem cell population maintenance / negative regulation of retinoic acid receptor signaling pathway ...positive regulation of cytoplasmic mRNA processing body assembly / regulation of tyrosine phosphorylation of STAT protein / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / armadillo repeat domain binding / CCR4-NOT complex / RNA exonuclease activity / 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 / deadenylation-dependent decapping of nuclear-transcribed mRNA / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / P-body assembly / 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 / negative regulation of type I interferon-mediated signaling pathway / intracellular non-membrane-bounded organelle / positive regulation of viral genome replication / nuclear estrogen receptor binding / P-body / mRNA processing / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / defense response to virus / DNA-binding transcription factor binding / negative regulation of translation / molecular adaptor activity / nuclear body / nuclear speck / protein domain specific binding / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 6-like / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 6-like / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 6-like / CCR4-NOT transcription complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.38 Å
AuthorsBartlam, M. / Zhang, Q.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053
National Natural Science Foundation of China (NSFC)31800627
CitationJournal: Protein Sci. / Year: 2022
Title: Structure of the human Ccr4-Not nuclease module using X-ray crystallography and electron paramagnetic resonance spectroscopy distance measurements.
Authors: Zhang, Q. / Pavanello, L. / Potapov, A. / Bartlam, M. / Winkler, G.S.
History
DepositionOct 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CCR4-NOT transcription complex subunit 7
A: CCR4-NOT transcription complex subunit 1
C: CCR4-NOT transcription complex subunit 6-like


Theoretical massNumber of molelcules
Total (without water)122,4813
Polymers122,4813
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.989, 110.989, 242.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein CCR4-NOT transcription complex subunit 7 / BTG1-binding factor 1 / CCR4-associated factor 1 / CAF-1 / Caf1a


Mass: 32776.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT7, CAF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UIV1, poly(A)-specific ribonuclease
#2: Protein CCR4-NOT transcription complex subunit 1 / CCR4-associated factor 1 / Negative regulator of transcription subunit 1 homolog / NOT1H / hNOT1


Mass: 26628.979 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 BL21(DE3) (bacteria) / References: UniProt: A5YKK6
#3: Protein CCR4-NOT transcription complex subunit 6-like / Carbon catabolite repressor protein 4 homolog B


Mass: 63076.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 8% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 4.38→50 Å / Num. obs: 10302 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 161.92 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.05 / Net I/σ(I): 27.3
Reflection shellResolution: 4.38→4.48 Å / Num. unique obs: 493 / CC1/2: 0.93 / Rpim(I) all: 0.177

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B8C, 4GMJ

4b8c

4gmj


Resolution: 4.38→38.74 Å / SU ML: 0.5167 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.5109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3239 1009 9.99 %
Rwork0.2625 9094 -
obs0.2687 10103 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 198.04 Å2
Refinement stepCycle: LAST / Resolution: 4.38→38.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 0 0 5449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565564
X-RAY DIFFRACTIONf_angle_d0.96057529
X-RAY DIFFRACTIONf_chiral_restr0.065839
X-RAY DIFFRACTIONf_plane_restr0.0071964
X-RAY DIFFRACTIONf_dihedral_angle_d9.3148719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.38-4.610.31391320.26771213X-RAY DIFFRACTION93.21
4.61-4.90.33131410.24131272X-RAY DIFFRACTION98.88
4.9-5.280.29111440.23681293X-RAY DIFFRACTION99.24
5.28-5.810.29971450.27131299X-RAY DIFFRACTION98.7
5.81-6.640.33881440.27391289X-RAY DIFFRACTION98.49
6.65-8.360.30091480.27081338X-RAY DIFFRACTION99.13
8.36-38.740.34391550.26381390X-RAY DIFFRACTION96.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.256505677981.07605876922-0.6487470071230.430999478934-0.54714167442.316916785910.3080302330350.07422607683330.565092313337-0.120358200781-0.1907302948840.0390091537840.02451242116010.1613036936120.0002229250661241.387441730.0003175783835850.008784658029811.60371453692-0.03897981419941.51243679637141.9753445739.58200991436275.4446203
21.336811098561.19738887506-0.6211824869344.876285935260.3695852170270.490368802180.07551782732640.0856102164498-0.2197606155110.1910350734820.0984409107542-0.6789394311710.209402486661-0.2140524728940.0002893920537881.313852967340.0595376307422-0.1974031477891.628638070430.2271177593791.5549473815159.724840102-7.67994181495298.462080266
35.096192042871.25498101564-2.577007136761.0978845828-1.516730437263.716837162140.1631983680330.05084657478990.3854390240540.644338841475-0.0797859744240.224883741226-0.832955355607-0.0320905916344-0.0009029608681531.9622813530.0508406860463-0.2287751994131.50014817839-0.004753196487552.13222681622109.61777055120.0357029401304.171233738
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 10 through 280)BA10 - 2801 - 264
22(chain 'A' and resid 1089 through 1317)AB1089 - 13171 - 229
33(chain 'C' and resid 37 through 526)CC37 - 5261 - 180

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