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- PDB-5aie: Not4 ring domain in complex with Ubc4 -

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Basic information

Entry
Database: PDB / ID: 5aie
TitleNot4 ring domain in complex with Ubc4
Components
  • GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
  • UBIQUITIN-CONJUGATING ENZYME E2 4
KeywordsLIGASE / SIGNALING PROTEIN / NOT4 RING DOMAIN / UBC4 / E2-E3 LIGASE
Function / homology
Function and homology information


deadenylation-independent decapping of nuclear-transcribed mRNA / Peroxisomal protein import / CCR4-NOT core complex / CCR4-NOT complex / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme ...deadenylation-independent decapping of nuclear-transcribed mRNA / Peroxisomal protein import / CCR4-NOT core complex / CCR4-NOT complex / cytoplasm protein quality control by the ubiquitin-proteasome system / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ribosome-associated ubiquitin-dependent protein catabolic process / E2 ubiquitin-conjugating enzyme / proteasome binding / ubiquitin conjugating enzyme activity / protein monoubiquitination / rescue of stalled ribosome / ubiquitin ligase complex / ubiquitin binding / proteasomal protein catabolic process / positive regulation of transcription elongation by RNA polymerase II / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ubiquitin protein ligase binding / RNA binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RING/Ubox like zinc-binding domain / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...RING/Ubox like zinc-binding domain / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 4 / General negative regulator of transcription subunit 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBhaskar, V. / Basquin, J. / Conti, E.
CitationJournal: Structure / Year: 2015
Title: Architecture of the Ubiquitylation Module of the Yeast Ccr4-not Complex.
Authors: Bhaskar, V. / Basquin, J. / Conti, E.
History
DepositionFeb 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
B: UBIQUITIN-CONJUGATING ENZYME E2 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2814
Polymers24,1502
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.112, 107.112, 62.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 / NOT4 / MODULATOR OF TRANSCRIPTION 2


Mass: 6796.774 Da / Num. of mol.: 1 / Fragment: RING DOMAIN, RESIDUES 30-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P34909
#2: Protein UBIQUITIN-CONJUGATING ENZYME E2 4 / UBC4 / UBIQUITIN CARRIER PROTEIN 4 / UBIQUITIN-PROTEIN LIGASE 4


Mass: 17353.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P15731, ubiquitin-protein ligase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsRSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE TGSTGSTETG RESIDUES ARE THE ARTIFICIAL LINKER ...RSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE TGSTGSTETG RESIDUES ARE THE ARTIFICIAL LINKER USED TO FUSE THE C-TERMINUS OF THE RING DOMAIN OF NOT4 WITH THE N- TERMINAL METHIONINE OF THE UBC4

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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: 2.85 Å3/Da / Density % sol: 56.86 % / Description: NONE
Crystal growpH: 8.5
Details: 10% (W/V) PEG 8000, 0.02 M OF L-NA-GLUTAMATE, 0.02 M OF ALANINE (RACEMIC), 0.02 M OF GLYCINE, 0.02 M OF LYSINE HCL (RACEMIC), 0.02 M OF SERINE (RACEMIC), 0.1 M BICINE PH 8.5 AND 20% (W/V) ...Details: 10% (W/V) PEG 8000, 0.02 M OF L-NA-GLUTAMATE, 0.02 M OF ALANINE (RACEMIC), 0.02 M OF GLYCINE, 0.02 M OF LYSINE HCL (RACEMIC), 0.02 M OF SERINE (RACEMIC), 0.1 M BICINE PH 8.5 AND 20% (W/V) ETHYLENE GLYCOL AS CRYSTALLIZATION BUFFER AT ROOM TEMPERATURE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99995
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 10, 2014
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2.8→53.56 Å / Num. obs: 6541 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.35
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 10 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.1 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→53.556 Å / SU ML: 0.45 / σ(F): 1.47 / Phase error: 38.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1200 9.2 %
Rwork0.22 --
obs0.2246 6505 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→53.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1573 0 2 0 1575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021621
X-RAY DIFFRACTIONf_angle_d0.5252217
X-RAY DIFFRACTIONf_dihedral_angle_d10.503589
X-RAY DIFFRACTIONf_chiral_restr0.023239
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7969-2.90890.4471280.41931223X-RAY DIFFRACTION94
2.9089-3.04130.36791240.33261316X-RAY DIFFRACTION98
3.0413-3.20160.40511330.31151295X-RAY DIFFRACTION100
3.2016-3.40210.30261310.29731334X-RAY DIFFRACTION99
3.4021-3.66480.27471400.27041339X-RAY DIFFRACTION98
3.6648-4.03350.30551390.251282X-RAY DIFFRACTION99
4.0335-4.61680.31861580.20371314X-RAY DIFFRACTION100
4.6168-5.81560.24191220.21111328X-RAY DIFFRACTION100
5.8156-53.56580.19781250.16041345X-RAY DIFFRACTION100

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