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- PDB-7ax1: Crystal structure of the human CCR4-CAF1 complex -

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Basic information

Entry
Database: PDB / ID: 7ax1
TitleCrystal structure of the human CCR4-CAF1 complex
Components
  • CCR4-NOT transcription complex subunit 6
  • CCR4-NOT transcription complex subunit 7
KeywordsRNA BINDING PROTEIN / Deadenylation / mRNA decay / CCR4-NOT complex / EEP hydrolase / DEDDh hydrolase
Function / homology
Function and homology information


regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, no-go decay / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / RNA exonuclease activity / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening ...regulation of tyrosine phosphorylation of STAT protein / positive regulation of cytoplasmic mRNA processing body assembly / nuclear-transcribed mRNA catabolic process, no-go decay / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / RNA exonuclease activity / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / : / Deadenylation of mRNA / deadenylation-dependent decapping of nuclear-transcribed mRNA / miRNA-mediated post-transcriptional gene silencing / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / intracellular non-membrane-bounded organelle / negative regulation of type I interferon-mediated signaling pathway / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / positive regulation of viral genome replication / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / nuclear receptor coactivator activity / P-body / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / DNA-binding transcription factor binding / defense response to virus / nuclear body / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / RNA binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT transcription complex subunit 6 / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...CCR4-NOT transcription complex subunit 6 / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 7 / CCR4-NOT transcription complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, Y. / Khazina, E. / Weichenrieder, O.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structure and functional properties of the human CCR4-CAF1 deadenylase complex.
Authors: Chen, Y. / Khazina, E. / Izaurralde, E. / Weichenrieder, O.
History
DepositionNov 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 30, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 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

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Assembly

Deposited unit
A: CCR4-NOT transcription complex subunit 6
B: CCR4-NOT transcription complex subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4084
Polymers97,3602
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-25 kcal/mol
Surface area37420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.850, 63.260, 113.070
Angle α, β, γ (deg.)90.000, 106.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CCR4-NOT transcription complex subunit 6 / CCR4 carbon catabolite repression 4-like / Carbon catabolite repressor protein 4 homolog / ...CCR4 carbon catabolite repression 4-like / Carbon catabolite repressor protein 4 homolog / Cytoplasmic deadenylase


Mass: 64049.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FIRST SIX AMINO ACIDS GPHMLE REMAIN FROM THE PURIFICATION TAG.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6, CCR4, CCR4a, KIAA1194 / Plasmid: pET-MCN / Details (production host): pnEA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q9ULM6, poly(A)-specific ribonuclease
#2: Protein CCR4-NOT transcription complex subunit 7 / BTG1-binding factor 1 / CCR4-associated factor 1 / CAF-1 / Caf1a


Mass: 33310.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE FIRST SIX AMINO ACIDS GPHMLE REMAIN FROM THE PURIFICATION TAG.
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT7, CAF1 / Plasmid: pET-MCN / Details (production host): pnYC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: Q9UIV1, poly(A)-specific ribonuclease
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 0.1M MgCl2, 8% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.3→71.74 Å / Num. obs: 15515 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 150.53 Å2 / CC1/2: 0.999 / Rsym value: 0.066 / Net I/σ(I): 11.8
Reflection shellResolution: 3.3→3.39 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1174 / CC1/2: 0.29 / Rsym value: 1.505 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GMJ,4B8C,3NGN

4gmj

4b8c

3ngn


Resolution: 3.3→71.724 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.97 / Stereochemistry target values: ML / Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.2758 776 5 %
Rwork0.2481 14734 -
obs0.2497 15510 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 360.52 Å2 / Biso mean: 163.6747 Å2 / Biso min: 68.2 Å2
Refinement stepCycle: final / Resolution: 3.3→71.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6231 0 2 0 6233
Biso mean--139.54 --
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036371
X-RAY DIFFRACTIONf_angle_d0.5028616
X-RAY DIFFRACTIONf_chiral_restr0.037947
X-RAY DIFFRACTIONf_plane_restr0.0041104
X-RAY DIFFRACTIONf_dihedral_angle_d10.2093829
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3001-3.50680.48851290.43552450100
3.5068-3.77760.37751280.33122429100
3.7776-4.15770.32131270.28532430100
4.1577-4.75920.25821300.22872437100
4.7592-5.99560.27641300.24782470100
5.9956-71.7240.24371320.2192251899

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