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- PDB-9wq4: Crystal structure of CNOT6L and Cpd1 complex -

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Basic information

Entry
Database: PDB / ID: 9wq4
TitleCrystal structure of CNOT6L and Cpd1 complex
ComponentsCCR4-NOT transcription complex subunit 6-like
KeywordsHYDROLASE / Inhibitor / complex
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / 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 / mRNA processing ...positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / 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 / mRNA processing / regulation of translation / 3'-5'-RNA exonuclease activity / positive regulation of cell population proliferation / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 6-like / : / 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
Similarity search - Domain/homology
: / CCR4-NOT transcription complex subunit 6-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, H.L. / Yang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of CNOT6L and Cpd1 complex
Authors: Zhang, H.L. / Yang, S.Y.
History
DepositionSep 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 6-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5314
Polymers45,1411
Non-polymers3903
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-20 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.171, 77.171, 169.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein CCR4-NOT transcription complex subunit 6-like / Carbon catabolite repressor protein 4 homolog B


Mass: 45140.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease
#2: Chemical ChemComp-A1EX3 / 4-[(4-chlorophenyl)methyl]-1-furo[3,2-c]pyridin-4-yl-piperidin-4-amine


Mass: 341.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20ClN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes, pH 7.5, 1.1M ammonium tartrate, 0.2M NDSB-201

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23653 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 37.12 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 17.66
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.01 / Num. unique obs: 1120 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→26.06 Å / SU ML: 0.2869 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 1191 5.23 %
Rwork0.206 21569 -
obs0.2086 22760 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.88 Å2
Refinement stepCycle: LAST / Resolution: 2.4→26.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 26 68 2767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242764
X-RAY DIFFRACTIONf_angle_d1.40543748
X-RAY DIFFRACTIONf_chiral_restr0.1329412
X-RAY DIFFRACTIONf_plane_restr0.0099475
X-RAY DIFFRACTIONf_dihedral_angle_d8.9543359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50.3195860.26942093X-RAY DIFFRACTION85.02
2.5-2.610.30411350.23672285X-RAY DIFFRACTION94.31
2.61-2.750.26011320.24272369X-RAY DIFFRACTION96.98
2.75-2.920.3311420.24972386X-RAY DIFFRACTION97.38
2.92-3.140.29851580.23452373X-RAY DIFFRACTION97.91
3.14-3.460.27971220.21662462X-RAY DIFFRACTION98.97
3.46-3.960.26181290.19362500X-RAY DIFFRACTION99.66
3.96-4.980.2031350.15872504X-RAY DIFFRACTION99.58
4.98-26.060.21311520.20062597X-RAY DIFFRACTION98.11

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