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- PDB-9jnj: Crystal structure of Human Cnot9 -

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Basic information

Entry
Database: PDB / ID: 9jnj
TitleCrystal structure of Human Cnot9
ComponentsCCR4-NOT transcription complex subunit 9
KeywordsPEPTIDE BINDING PROTEIN / CCR4-NOT complex / mRNA degradation
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / epidermal growth factor receptor binding / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain ...CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / epidermal growth factor receptor binding / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / transcription coactivator activity / negative regulation of translation / protein domain specific binding / protein homodimerization activity / protein-containing complex / nucleus / membrane / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, K.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of Human Cnot9
Authors: Yang, K.L.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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 9
B: CCR4-NOT transcription complex subunit 9
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 9


Theoretical massNumber of molelcules
Total (without water)122,0864
Polymers122,0864
Non-polymers00
Water8,575476
1
A: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 9


Theoretical massNumber of molelcules
Total (without water)61,0432
Polymers61,0432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-18 kcal/mol
Surface area23870 Å2
MethodPISA
2
B: CCR4-NOT transcription complex subunit 9
C: CCR4-NOT transcription complex subunit 9


Theoretical massNumber of molelcules
Total (without water)61,0432
Polymers61,0432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-18 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.069, 68.773, 69.530
Angle α, β, γ (deg.)118.02, 94.29, 93.67
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CCR4-NOT transcription complex subunit 9 / Cell differentiation protein RQCD1 homolog / Rcd-1


Mass: 30521.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92600
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulphate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→47.71 Å / Num. obs: 72371 / % possible obs: 97.1 % / Redundancy: 3.5 % / CC1/2: 0.995 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.04 Å / Num. unique obs: 4470 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2→42.64 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1997 2.76 %
Rwork0.1977 --
obs0.1988 72360 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8482 0 0 476 8958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088642
X-RAY DIFFRACTIONf_angle_d0.92111734
X-RAY DIFFRACTIONf_dihedral_angle_d16.6823241
X-RAY DIFFRACTIONf_chiral_restr0.0511417
X-RAY DIFFRACTIONf_plane_restr0.0091463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28651390.23674990X-RAY DIFFRACTION96
2.05-2.110.32121470.22944969X-RAY DIFFRACTION96
2.11-2.170.32341430.2214998X-RAY DIFFRACTION96
2.17-2.240.25221420.22515019X-RAY DIFFRACTION97
2.24-2.320.2811420.21184979X-RAY DIFFRACTION97
2.32-2.410.26871450.20695002X-RAY DIFFRACTION97
2.41-2.520.25561420.20395044X-RAY DIFFRACTION97
2.52-2.650.24511390.20815026X-RAY DIFFRACTION97
2.65-2.820.22651410.2125028X-RAY DIFFRACTION97
2.82-3.040.2371400.21075058X-RAY DIFFRACTION97
3.04-3.340.26461470.21095036X-RAY DIFFRACTION97
3.34-3.820.21221460.18525075X-RAY DIFFRACTION98
3.83-4.820.19891430.16835064X-RAY DIFFRACTION98
4.82-42.640.21531410.18615075X-RAY DIFFRACTION98

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