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- PDB-4ct7: CNOT9-CNOT1 complex with bound tryptophan -

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Basic information

Entry
Database: PDB / ID: 4ct7
TitleCNOT9-CNOT1 complex with bound tryptophan
Components
  • CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
  • CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
KeywordsTRANSCRIPTION / CNOT1-CN9DB-DOMAIN / TRYPTOPHANE / MES
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / 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 / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway ...positive regulation of cytoplasmic mRNA processing body assembly / armadillo repeat domain binding / CCR4-NOT core complex / 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 / sex differentiation / negative regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated post-transcriptional gene silencing / trophectodermal cell differentiation / Deadenylation of mRNA / nuclear retinoic acid receptor binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / peroxisomal membrane / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / epidermal growth factor receptor binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of peptidyl-serine phosphorylation / nuclear estrogen receptor binding / P-body / kinase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cytokine-mediated signaling pathway / 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
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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
TRYPTOPHAN / CCR4-NOT transcription complex subunit 1 / CCR4-NOT transcription complex subunit 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsBasquin, J. / Ozgur, S. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression.
Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W.
History
DepositionMar 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 1
B: CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6194
Polymers58,2192
Non-polymers3992
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-19.8 kcal/mol
Surface area23280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.031, 66.984, 72.653
Angle α, β, γ (deg.)90.00, 99.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2183-

HOH

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Components

#1: Protein CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 / CCR4-ASSOCIATED FACTOR 1 / NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 HOMOLOG / NOT1H / HNOT1 / CNOT1-CN9BD


Mass: 27470.666 Da / Num. of mol.: 1 / Fragment: CNOT1-CN9BD DOMAIN RESIDUES 1352-1594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_GST / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A5YKK6
#2: Protein CELL DIFFERENTIATION PROTEIN RCD1 HOMOLOG / RCD-1 / CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 9 / CNOT9


Mass: 30748.760 Da / Num. of mol.: 1 / Fragment: CNOT9, RESIDUES 16-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q92600
#3: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.6 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 6
Details: 20 % PEG 3350, 200 MM AMMONIUM SULFATE, 50 MM MES PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.897→48.27 Å / Num. obs: 54804 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3 / Redundancy: 4.6 % / Biso Wilson estimate: 37.07 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 1.897→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FV2

2fv2


Resolution: 1.897→48.271 Å / SU ML: 0.32 / σ(F): 1.21 / Phase error: 26.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 5630 5 %
Rwork0.1833 --
obs0.1852 54804 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.897→48.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 26 415 4402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084065
X-RAY DIFFRACTIONf_angle_d1.1045519
X-RAY DIFFRACTIONf_dihedral_angle_d13.9641533
X-RAY DIFFRACTIONf_chiral_restr0.043646
X-RAY DIFFRACTIONf_plane_restr0.005705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8972-1.91870.65921360.56812574X-RAY DIFFRACTION72
1.9187-1.94130.45461850.46143518X-RAY DIFFRACTION100
1.9413-1.9650.45061970.37963730X-RAY DIFFRACTION100
1.965-1.98980.35751810.36043457X-RAY DIFFRACTION100
1.9898-2.0160.41311930.32463696X-RAY DIFFRACTION100
2.016-2.04360.29541810.30453524X-RAY DIFFRACTION100
2.0436-2.07280.32881950.29083630X-RAY DIFFRACTION100
2.0728-2.10380.33421930.2873645X-RAY DIFFRACTION100
2.1038-2.13660.26051880.26483564X-RAY DIFFRACTION100
2.1366-2.17170.27451900.25693598X-RAY DIFFRACTION100
2.1717-2.20910.2751920.24843610X-RAY DIFFRACTION100
2.2091-2.24930.27281930.23163609X-RAY DIFFRACTION100
2.2493-2.29260.30691860.22583563X-RAY DIFFRACTION100
2.2926-2.33930.25851900.2163638X-RAY DIFFRACTION100
2.3393-2.39020.24711880.20083586X-RAY DIFFRACTION100
2.3902-2.44580.24021910.19643621X-RAY DIFFRACTION100
2.4458-2.5070.21311920.18853598X-RAY DIFFRACTION100
2.507-2.57480.22321930.18783588X-RAY DIFFRACTION100
2.5748-2.65050.24541880.18543575X-RAY DIFFRACTION100
2.6505-2.73610.23171900.18583641X-RAY DIFFRACTION100
2.7361-2.83380.25641900.18223584X-RAY DIFFRACTION100
2.8338-2.94730.22221900.18433582X-RAY DIFFRACTION99
2.9473-3.08140.23111860.18193609X-RAY DIFFRACTION99
3.0814-3.24380.19761900.18183613X-RAY DIFFRACTION99
3.2438-3.4470.2321860.1733562X-RAY DIFFRACTION99
3.447-3.71310.19271910.15963574X-RAY DIFFRACTION99
3.7131-4.08650.17561880.14523571X-RAY DIFFRACTION99
4.0865-4.67750.18481890.12663593X-RAY DIFFRACTION99
4.6775-5.89140.2081850.1533589X-RAY DIFFRACTION100
5.8914-48.2870.14681930.14953608X-RAY DIFFRACTION100
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)
16.7171.7491-4.17634.5446-1.20934.1324-0.085-0.2568-0.60860.0070.02340.47580.166-0.30550.08390.497-0.0197-0.11770.3725-0.03570.53524.92892.0966-0.1013
23.01280.70041.80171.68740.11981.59350.0139-0.05530.2799-0.112-0.00840.39220.0629-0.2448-0.00310.2886-0.0258-0.01420.2464-0.0040.326537.268114.62840.1653
35.91060.78720.68641.4033-0.17621.18660.06270.04020.0132-0.21240.00950.05980.18710.0116-0.06020.30790.0211-0.00370.2044-0.04010.218448.918412.2940.2704
44.13580.3137-0.63962.4656-0.29271.9563-0.0555-0.3107-0.2310.14410.0273-0.14850.15810.13190.0290.30570.0110.00540.25730.0330.238954.05711.752917.1744
53.4047-0.9614-2.07134.88591.24576.36530.0401-0.31130.22360.16790.01130.0235-0.1299-0.0072-0.03370.30650.02540.03590.2862-0.04720.288740.877833.349431.2484
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1352 THROUGH 1386 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1387 THROUGH 1476 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1477 THROUGH 1588 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 16 THROUGH 148 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 149 THROUGH 284 )

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