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- PDB-5dv4: Crystal structure of human CNOT6L in complex with neomycin -

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Basic information

Entry
Database: PDB / ID: 5dv4
TitleCrystal structure of human CNOT6L in complex with neomycin
ComponentsCCR4-NOT transcription complex subunit 6-like
KeywordsHYDROLASE / nuclease domain / deadenylase
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 / metal ion binding / nucleus / 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 / Leucine-rich repeat profile. ...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
NEOMYCIN / CCR4-NOT transcription complex subunit 6-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, Q. / Bartlam, M.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science & Technology 973 Project2014CB560709 China
CitationJournal: Febs Lett. / Year: 2016
Title: Structural basis for inhibition of the deadenylase activity of human CNOT6L
Authors: Zhang, Q. / Yan, D. / Guo, E. / Ding, B. / Yang, W. / Liu, R. / Yamamoto, T. / Bartlam, M.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9474
Polymers45,1411
Non-polymers8073
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-39 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.388, 77.388, 167.188
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-945-

HOH

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Components

#1: Protein CCR4-NOT transcription complex subunit 6-like / Carbon catabolite repressor protein 4 homolog B


Mass: 45140.500 Da / Num. of mol.: 1 / Mutation: UNP residues 158-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNOT6L, CCR4B / Production host: Escherichia coli (E. coli) / References: UniProt: Q96LI5, poly(A)-specific ribonuclease
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN / Neomycin


Mass: 614.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Hepes, 1.1M ammonium tartrate, 0.2M NDSB-201

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 54573 / % possible obs: 99.9 % / Redundancy: 10.2 % / Net I/σ(I): 50

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.465 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2013 3.7 %Random selection
Rwork0.1897 ---
obs0.1907 54475 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 52 304 3130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152913
X-RAY DIFFRACTIONf_angle_d1.8133948
X-RAY DIFFRACTIONf_dihedral_angle_d14.6241715
X-RAY DIFFRACTIONf_chiral_restr0.085440
X-RAY DIFFRACTIONf_plane_restr0.009497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.33661410.2993685X-RAY DIFFRACTION100
1.8451-1.8950.31420.26133694X-RAY DIFFRACTION100
1.895-1.95080.35191400.26033689X-RAY DIFFRACTION100
1.9508-2.01370.221420.19873684X-RAY DIFFRACTION100
2.0137-2.08570.23751440.19673735X-RAY DIFFRACTION100
2.0857-2.16920.24171420.19613705X-RAY DIFFRACTION100
2.1692-2.26790.26251440.20953704X-RAY DIFFRACTION100
2.2679-2.38740.23691440.18943707X-RAY DIFFRACTION100
2.3874-2.5370.21981410.19393747X-RAY DIFFRACTION100
2.537-2.73280.23531440.193763X-RAY DIFFRACTION100
2.7328-3.00770.24391460.19583773X-RAY DIFFRACTION100
3.0077-3.44260.20571420.18083785X-RAY DIFFRACTION100
3.4426-4.33610.17731490.15783835X-RAY DIFFRACTION100
4.3361-35.47220.19181520.1913956X-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)
14.7434-0.15820.40112.1719-0.13122.37520.0844-0.3039-0.4471-0.09390.24540.40130.3172-0.2526-0.18560.3194-0.1141-0.10690.29710.15830.3462-38.00540.87988.3374
21.22520.29890.09832.7963-0.21571.6179-0.03260.11960.0257-0.5510.20220.284-0.0688-0.1695-0.09020.3611-0.1092-0.12240.28070.09520.2696-37.452214.2776-2.5895
33.7315-0.37731.29733.1442-0.33294.1036-0.06580.00490.5716-0.22690.17340.7092-0.7566-0.44570.0580.41080.0368-0.00560.32270.13530.4633-46.08126.97496.7984
41.5687-1.04891.03411.7204-0.63132.57660.1075-0.3393-0.35380.09090.30060.67690.1385-0.5763-0.37260.2944-0.0964-0.02350.39720.20850.4461-44.24445.587414.4648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 169 through 231 )
2X-RAY DIFFRACTION2chain 'A' and (resid 232 through 367 )
3X-RAY DIFFRACTION3chain 'A' and (resid 368 through 465 )
4X-RAY DIFFRACTION4chain 'A' and (resid 466 through 540 )

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