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- PDB-4b89: MIF4G domain of the yeast Not1 -

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Basic information

Entry
Database: PDB / ID: 4b89
TitleMIF4G domain of the yeast Not1
ComponentsGENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / P-body / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / P-body / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / negative regulation of translation / molecular adaptor activity / regulation of cell cycle / regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / 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 transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
General negative regulator of transcription subunit 1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBasquin, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2012
Title: Architecture of the Nuclease Module of the Yeast Ccr4-not Complex: The not1-Caf1-Ccr4 Interaction.
Authors: Basquin, J. / Roudko, V.V. / Rode, M. / Basquin, C. / Seraphin, B. / Conti, E.
History
DepositionAug 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1


Theoretical massNumber of molelcules
Total (without water)28,5271
Polymers28,5271
Non-polymers00
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.758, 53.758, 187.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 / CELL DIVISION CYCLE PROTEIN 39 / NOT1


Mass: 28527.402 Da / Num. of mol.: 1 / Fragment: MIF4G, RESIDUES 755-1000
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Plasmid: PEC_SUMO_HT_A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS STAR / References: UniProt: P25655
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.43 Å3/Da / Density % sol: 49.3 % / Description: NONE
Crystal growpH: 7.5 / Details: 20% (W/V) PEG3350, 0.5 M NAI AND 50 MM TRIS PH 7.5

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→93.58 Å / Num. obs: 54005 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C ALPHA TRACE FROM EXPERIMENTAL (SAD) MAP.

Resolution: 1.5→46.788 Å / SU ML: 0.2 / σ(F): 2.01 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 4177 5 %
Rwork0.1846 --
obs0.1858 83905 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.929 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.175 Å20 Å20 Å2
2--0.175 Å20 Å2
3----0.3499 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 0 328 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051883
X-RAY DIFFRACTIONf_angle_d0.9932554
X-RAY DIFFRACTIONf_dihedral_angle_d11.489697
X-RAY DIFFRACTIONf_chiral_restr0.064305
X-RAY DIFFRACTIONf_plane_restr0.005314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.55360.20374140.19217961X-RAY DIFFRACTION100
1.5536-1.61580.21984220.18727965X-RAY DIFFRACTION100
1.6158-1.68940.19174200.18747983X-RAY DIFFRACTION100
1.6894-1.77840.21544100.18127978X-RAY DIFFRACTION100
1.7784-1.88990.21274240.17647962X-RAY DIFFRACTION100
1.8899-2.03580.20244260.17987963X-RAY DIFFRACTION100
2.0358-2.24070.19584170.17648016X-RAY DIFFRACTION100
2.2407-2.56490.2324170.17727956X-RAY DIFFRACTION100
2.5649-3.23130.19664160.18367952X-RAY DIFFRACTION100
3.2313-46.81130.2014110.18497992X-RAY DIFFRACTION100

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