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- PDB-9fl8: Stapled peptide bound to NOT9-NOT1 complex -

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Basic information

Entry
Database: PDB / ID: 9fl8
TitleStapled peptide bound to NOT9-NOT1 complex
Components
  • CCR4-NOT transcription complex subunit 1
  • CCR4-NOT transcription complex subunit 9
  • Protein bag of marbles
KeywordsRNA BINDING PROTEIN / protein-peptide interaction / inhibitor / CCR4-NOT
Function / homology
Function and homology information


male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of cytoplasmic mRNA processing body assembly / positive regulation of protein deubiquitination ...male germline stem cell symmetric division / cystoblast division / spectrosome / fusome organization / germarium-derived female germ-line cyst formation / negative regulation of peptidoglycan recognition protein signaling pathway / fusome / germ-line stem cell division / positive regulation of cytoplasmic mRNA processing body assembly / positive regulation of protein deubiquitination / cell competition in a multicellular organism / CCR4-NOT core complex / spermatogonial cell division / armadillo repeat domain binding / female germ-line stem cell asymmetric division / 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 / negative regulation of intracellular estrogen receptor signaling pathway / germ-line stem cell population maintenance / gamete generation / sex differentiation / positive regulation of stem cell differentiation / trophectodermal cell differentiation / miRNA-mediated post-transcriptional gene silencing / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of protein K63-linked deubiquitination / positive regulation of smoothened signaling pathway / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / epidermal growth factor receptor binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of epidermal growth factor receptor signaling pathway / oogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of peptidyl-serine phosphorylation / mRNA regulatory element binding translation repressor activity / ubiquitin binding / mRNA 3'-UTR binding / nuclear estrogen receptor binding / P-body / cytokine-mediated signaling pathway / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spermatogenesis / 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 / cytoplasm
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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
1,4-BUTANEDIOL / CCR4-NOT transcription complex subunit 1 / Protein bag of marbles / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPal, S. / Schmeing, S. / Gasper, R. / t Hart, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionHORIZON-MSCA-2021-PF-01-101061526European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Stapled Peptides as Inhibitors of mRNA Deadenylation.
Authors: Pal, S. / Gordijenko, I. / Schmeing, S. / Biswas, S. / Akbulut, Y. / Gasper, R. / 't Hart, P.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Protein bag of marbles
F: Protein bag of marbles
B: CCR4-NOT transcription complex subunit 9
A: CCR4-NOT transcription complex subunit 1
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,04812
Polymers121,5076
Non-polymers5416
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-66 kcal/mol
Surface area44660 Å2
Unit cell
Length a, b, c (Å)106.562, 106.562, 262.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein/peptide Protein bag of marbles / CAF40-binding motif domain peptide


Mass: 2063.458 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: P22745
#2: Protein CCR4-NOT transcription complex subunit 9 / Cell differentiation protein RQCD1 homolog / Rcd-1


Mass: 31072.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92600
#3: Protein CCR4-NOT transcription complex subunit 1 / CCR4-associated factor 1 / Negative regulator of transcription subunit 1 homolog / hNOT1


Mass: 27617.930 Da / Num. of mol.: 2
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 (E. coli) / References: UniProt: A5YKK6
#4: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.86 Å3/Da / Density % sol: 33.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5 / Details: 2M sodium formate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.64→131.286 Å / Num. obs: 26138 / % possible obs: 50.7 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.047 / Rrim(I) all: 0.208 / Net I/σ(I): 10.4
Reflection shellResolution: 2.645→2.97 Å / % possible obs: 8.8 % / Redundancy: 19.8 % / Rmerge(I) obs: 1.968 / Num. measured all: 25814 / Num. unique obs: 1307 / Rpim(I) all: 0.45 / Rrim(I) all: 2.02 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→46.14 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1304 5 %
Rwork0.2028 --
obs0.2052 26063 50.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8359 0 36 46 8441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048610
X-RAY DIFFRACTIONf_angle_d0.65311661
X-RAY DIFFRACTIONf_dihedral_angle_d8.8331205
X-RAY DIFFRACTIONf_chiral_restr0.0381344
X-RAY DIFFRACTIONf_plane_restr0.0061503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.750.6277140.4682194X-RAY DIFFRACTION4
2.75-2.880.4977340.4127506X-RAY DIFFRACTION10
2.88-3.030.4758280.3508906X-RAY DIFFRACTION17
3.03-3.220.3275570.31691345X-RAY DIFFRACTION25
3.22-3.470.3704780.27821996X-RAY DIFFRACTION37
3.47-3.810.30542010.23413353X-RAY DIFFRACTION62
3.81-4.360.2632930.19765250X-RAY DIFFRACTION97
4.37-5.50.24632850.18485492X-RAY DIFFRACTION100
5.5-46.140.19783140.17915717X-RAY DIFFRACTION100

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