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- PDB-3ngo: Crystal structure of the human CNOT6L nuclease domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 3ngo
TitleCrystal structure of the human CNOT6L nuclease domain in complex with poly(A) DNA
Components
  • 5'-D(*AP*AP*AP*A)-3'
  • CCR4-NOT transcription complex subunit 6-like
KeywordsHYDROLASE/DNA / PROTEIN-ssDNA COMPLEX / HYDROLASE-DNA complex
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / 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 / mRNA processing ...positive regulation of cytoplasmic mRNA processing body assembly / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / 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 / mRNA processing / regulation of translation / positive regulation of cell population proliferation / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 6-like / : / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / 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-like / : / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / 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 / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / CCR4-NOT transcription complex subunit 6-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, H. / Morita, M. / Yang, W. / Bartlam, M. / Yamamoto, T. / Rao, Z.
CitationJournal: Embo J. / Year: 2010
Title: Crystal structure of the human CNOT6L nuclease domain reveals strict poly(A) substrate specificity.
Authors: Wang, H. / Morita, M. / Yang, X. / Suzuki, T. / Yang, W. / Wang, J. / Ito, K. / Wang, Q. / Zhao, C. / Bartlam, M. / Yamamoto, T. / Rao, Z.
History
DepositionJun 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site
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_asym_id / _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_asym_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_asym_id / _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_asym_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_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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 6-like
B: 5'-D(*AP*AP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3974
Polymers46,3482
Non-polymers492
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.373, 77.373, 167.177
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 CCR4-NOT transcription complex subunit 6-like / CNOT6L / Carbon catabolite repressor protein 4 homolog B


Mass: 45140.500 Da / Num. of mol.: 1 / Fragment: Nuclease Domain (UNP RESIDUES 158-555)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96LI5, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*AP*AP*AP*A)-3'


Mass: 1207.870 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 3.12 Å3/Da / Density % sol: 60.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes, pH 7.5, 1.1M ammonium tartrate, 0.2M NDSB-201, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 30308 / Num. obs: 30217 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 52.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1466 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.951 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26314 1522 5 %RANDOM
Rwork0.21475 ---
obs0.21718 28627 99.56 %-
all-28753 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.014 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.61 Å20 Å2
2---1.21 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2722 54 2 112 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222870
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9783897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0085335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.32224.776134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85815489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0561510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212144
X-RAY DIFFRACTIONr_mcbond_it1.0171.51692
X-RAY DIFFRACTIONr_mcangle_it1.89822746
X-RAY DIFFRACTIONr_scbond_it2.7531178
X-RAY DIFFRACTIONr_scangle_it4.5064.51151
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 113 -
Rwork0.276 2060 -
obs--98.15 %

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