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- PDB-9wq1: Crystal structure of CNOT6L and YL-333P complex -

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Basic information

Entry
Database: PDB / ID: 9wq1
TitleCrystal structure of CNOT6L and YL-333P complex
ComponentsCCR4-NOT transcription complex subunit 6-like
KeywordsHYDROLASE / Inhibitor / complex / RNA BINDING PROTEIN
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: 2.09 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 333P 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)45,6784
Polymers45,1411
Non-polymers5373
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-20 kcal/mol
Surface area15200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.737, 78.737, 171.726
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1EX4 / 6-[4-[[4-azanyl-1-[7-[bis(fluoranyl)methyl]pyrrolo[2,3-d]pyrimidin-4-yl]piperidin-4-yl]methyl]phenyl]-2,3-dihydroisoindol-1-one


Mass: 488.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26F2N6O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 37580 / % possible obs: 100 % / Redundancy: 18.79 % / Biso Wilson estimate: 33.08 Å2 / CC1/2: 0.9752 / CC star: 0.9937 / Net I/σ(I): 6.44
Reflection shellResolution: 2.09→2.14 Å / Num. unique obs: 2717 / CC1/2: 0.0164 / CC star: 0.1797 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→43.84 Å / SU ML: 0.7814 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 54.4201
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3186 1683 4.81 %
Rwork0.2741 33303 -
obs0.2763 34986 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.78 Å2
Refinement stepCycle: LAST / Resolution: 2.09→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 38 57 2781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922798
X-RAY DIFFRACTIONf_angle_d1.28323796
X-RAY DIFFRACTIONf_chiral_restr0.1232413
X-RAY DIFFRACTIONf_plane_restr0.0077480
X-RAY DIFFRACTIONf_dihedral_angle_d12.61363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.7281110.72155X-RAY DIFFRACTION73.33
2.15-2.220.43971130.45012357X-RAY DIFFRACTION80.46
2.22-2.30.44641310.44862647X-RAY DIFFRACTION90.58
2.3-2.390.46291550.43182742X-RAY DIFFRACTION93.06
2.39-2.50.49491330.41032719X-RAY DIFFRACTION93.2
2.5-2.630.37581350.39162819X-RAY DIFFRACTION94.5
2.63-2.790.38991430.38162818X-RAY DIFFRACTION96.48
2.79-3.010.37421360.32242928X-RAY DIFFRACTION97.49
3.01-3.310.31251790.29652918X-RAY DIFFRACTION98.95
3.31-3.790.30681140.23383017X-RAY DIFFRACTION99.27
3.79-4.770.24411340.20283032X-RAY DIFFRACTION99.69
4.78-43.840.27011990.20233151X-RAY DIFFRACTION99.79

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