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- PDB-6hom: Drosophila NOT4 CBM peptide bound to human CAF40 -

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Basic information

Entry
Database: PDB / ID: 6hom
TitleDrosophila NOT4 CBM peptide bound to human CAF40
Components(CCR4-NOT transcription complex subunit ...) x 2
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION / UBIQUITINATION
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / 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 / positive regulation of epidermal growth factor receptor signaling pathway ...CCR4-NOT core complex / CCR4-NOT complex / negative regulation of intracellular estrogen receptor signaling pathway / nuclear-transcribed mRNA poly(A) tail shortening / sex differentiation / 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 / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / nuclear receptor coactivator activity / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / ubiquitin-protein transferase activity / positive regulation of peptidyl-serine phosphorylation / negative regulation of translation / protein ubiquitination / protein domain specific binding / protein homodimerization activity / protein-containing complex / RNA binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. ...CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / RNA recognition motif domain, eukaryote / RNA recognition motif / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 4, isoform L / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHomo sapiens (human)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRaisch, T. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Genes Dev. / Year: 2019
Title: A conserved CAF40-binding motif in metazoan NOT4 mediates association with the CCR4-NOT complex.
Authors: Keskeny, C. / Raisch, T. / Sgromo, A. / Igreja, C. / Bhandari, D. / Weichenrieder, O. / Izaurralde, E.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 4, isoform L
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 4, isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5279
Polymers68,0254
Non-polymers5025
Water3,207178
1
A: CCR4-NOT transcription complex subunit 9
B: CCR4-NOT transcription complex subunit 4, isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3275
Polymers34,0122
Non-polymers3143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-30 kcal/mol
Surface area14110 Å2
MethodPISA
2
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 4, isoform L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2014
Polymers34,0122
Non-polymers1882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-21 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.920, 109.640, 69.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-447-

HOH

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Components

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CCR4-NOT transcription complex subunit ... , 2 types, 4 molecules ACBD

#1: 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
Details: The first six residues (GPHMLE) remain from the expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT9, RCD1, RQCD1 / Plasmid: PETMCN (PNEA) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q92600
#2: Protein/peptide CCR4-NOT transcription complex subunit 4, isoform L


Mass: 2940.171 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: M9PCL9

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Non-polymers , 4 types, 183 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris/Cl, pH 5.5, 0.2 M ammonium sulfate, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2016 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38143 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.99 / Rsym value: 0.07 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2780 / CC1/2: 0.556 / Rsym value: 0.914 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FV2, chain A

2fv2


Resolution: 2.1→48.16 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8
RfactorNum. reflection% reflection
Rfree0.2215 1870 4.91 %
Rwork0.191 --
obs0.1926 38096 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 29 178 4961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024877
X-RAY DIFFRACTIONf_angle_d0.516626
X-RAY DIFFRACTIONf_dihedral_angle_d13.0283000
X-RAY DIFFRACTIONf_chiral_restr0.037784
X-RAY DIFFRACTIONf_plane_restr0.004838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.32721190.28492767X-RAY DIFFRACTION100
2.1568-2.22020.31041550.25752725X-RAY DIFFRACTION100
2.2202-2.29190.25611280.24822763X-RAY DIFFRACTION100
2.2919-2.37380.28541490.22732765X-RAY DIFFRACTION100
2.3738-2.46880.24971510.22212735X-RAY DIFFRACTION100
2.4688-2.58120.2521460.21352764X-RAY DIFFRACTION100
2.5812-2.71730.29921470.21532769X-RAY DIFFRACTION100
2.7173-2.88750.2541360.20892774X-RAY DIFFRACTION99
2.8875-3.11040.28021360.20752778X-RAY DIFFRACTION100
3.1104-3.42340.23231460.19612791X-RAY DIFFRACTION100
3.4234-3.91850.20551480.17662801X-RAY DIFFRACTION99
3.9185-4.93620.17521570.14932839X-RAY DIFFRACTION100
4.9362-48.1730.1791520.17672955X-RAY DIFFRACTION99
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)
11.6089-0.63960.49761.4301-0.47662.49040.04630.12210.0724-0.08080.00140.1346-0.1708-0.0697-0.04020.26210.01780.00770.23430.03990.28675.208524.455112.3499
23.21311.595-1.38625.823-2.32626.37860.02450.04580.08040.00040.17050.7126-0.1804-0.7708-0.21350.37170.1128-0.02060.49250.11580.6559-9.108623.339821.4522
31.6333-0.08780.72811.6019-0.04813.36370.0714-0.0764-0.10330.16090.0963-0.16560.26310.1406-0.10170.26260.0243-0.04930.22970.01730.355825.64776.081535.4203
45.83791.43432.61294.05670.22036.9333-0.07860.2091-0.7364-0.2634-0.1202-0.49490.57510.89090.18930.47890.1987-0.04020.55290.01280.812325.6383-5.917324.9408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 13 through 285)
2X-RAY DIFFRACTION2(chain 'B' and resid 814 through 838)
3X-RAY DIFFRACTION3(chain 'C' and resid 15 through 285)
4X-RAY DIFFRACTION4(chain 'D' and resid 813 through 838)

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