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

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Basic information

Entry
Database: PDB / ID: 6hon
TitleDrosophila NOT4 CBM peptide bound to human CAF40
Components
  • CCR4-NOT transcription complex subunit 4, isoform L
  • CCR4-NOT transcription complex subunit 9
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION / UBIQUITINATION
Function / homology
Function and homology information


CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / 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 / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / 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: 2.2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)68,1197
Polymers68,0254
Non-polymers943
Water1,15364
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)34,1065
Polymers34,0122
Non-polymers943
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-33 kcal/mol
Surface area14170 Å2
MethodPISA
2
C: CCR4-NOT transcription complex subunit 9
D: CCR4-NOT transcription complex subunit 4, isoform L


Theoretical massNumber of molelcules
Total (without water)34,0122
Polymers34,0122
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-11 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.630, 90.320, 196.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-301-

NA

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Components

#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) / Strain (production host): BL21(DE3) / 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.9 M K2HPO4, 0.3 M NaH2PO4

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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: 2.2→50 Å / Num. obs: 39129 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 56.7 Å2 / CC1/2: 1 / Rsym value: 0.065 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.25 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2831 / CC1/2: 0.899 / Rsym value: 1.57

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fv2, chain A

2fv2


Resolution: 2.2→49.25 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9269 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.202 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1907 4.87 %RANDOM
Rwork0.1928 ---
obs0.1947 39127 99.88 %-
Displacement parametersBiso mean: 81 Å2
Baniso -1Baniso -2Baniso -3
1--5.322 Å20 Å20 Å2
2---20.3523 Å20 Å2
3---25.6742 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 3 64 4805
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014828HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.046556HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1714SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes678HARMONIC5
X-RAY DIFFRACTIONt_it4828HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion17.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion650SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5597SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2755 123 4.34 %
Rwork0.2477 2709 -
all0.2488 2832 -
obs--99.79 %
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)
12.20930.192-0.79870.4747-0.16313.42670.04360.24190.21970.02590.0070.0414-0.5592-0.3431-0.0506-0.05590.1320.0218-0.15240.0165-0.18434.064593.8235210.52
24.3621-2.6806-1.79713.04331.88680.1201-0.0357-0.03220.03050.0087-0.0360.2518-0.2985-0.01730.0718-0.01250.20850.1129-0.11170.06260.0013-9.997791.5191219.965
31.5957-0.2529-0.0370.8961-0.19192.96730.0372-0.137-0.09110.0974-0.0036-0.14750.0650.6156-0.0336-0.1440.0873-0.04030.0082-0.0285-0.20725.228574.2339233.297
42.87770.3215-1.32942.35350.54140.0327-0.0478-0.0064-0.1719-0.0713-0.057-0.28370.11880.14680.1048-0.16310.2173-0.01230.1246-0.1129-0.043225.67562.4487222.115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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