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- PDB-4b8a: Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1 -

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Basic information

Entry
Database: PDB / ID: 4b8a
TitleStructure of yeast NOT1 MIF4G domain co-crystallized with CAF1
Components
  • GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
  • POLY(A) RIBONUCLEASE POP2
KeywordsTRANSCRIPTION/HYDROLASE / TRANSCRIPTION-HYDROLASE COMPLEX
Function / homology
Function and homology information


response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / : / nuclear-transcribed mRNA poly(A) tail shortening / mating projection tip / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / poly(A)-specific ribonuclease / CCR4-NOT core complex / poly(A)-specific ribonuclease activity / : / nuclear-transcribed mRNA poly(A) tail shortening / mating projection tip / 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 / 3'-5'-RNA exonuclease activity / negative regulation of translation / molecular adaptor activity / regulation of cell cycle / regulation of transcription by RNA polymerase II / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
CCR4-NOT transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 transcription complex subunit 1, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / 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 / Ribonuclease H-like superfamily/Ribonuclease H / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
General negative regulator of transcription subunit 1 / Poly(A) ribonuclease POP2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.1Aug 13, 2014Group: Atomic model
Revision 1.2Apr 20, 2016Group: Atomic model / Other
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
B: POLY(A) RIBONUCLEASE POP2


Theoretical massNumber of molelcules
Total (without water)61,6812
Polymers61,6812
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-9.2 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.850, 76.560, 109.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS STAR / References: UniProt: P25655
#2: Protein POLY(A) RIBONUCLEASE POP2 / CCR4-ASSOCIATED FACTOR 1


Mass: 33153.352 Da / Num. of mol.: 1 / Fragment: NUCLEASE DOMAIN, RESIDUES 151-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS STAR / References: UniProt: P39008, poly(A)-specific ribonuclease
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.53 Å3/Da / Density % sol: 51.51 % / Description: NONE
Crystal growpH: 8
Details: 8% (W/V) PEG 8000, 0.2 M NA MALONATE, 50 MM TRIS PH 8.0 AND 0.1% LOW MELTING AGAROSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.7 Å / Num. obs: 27615 / % possible obs: 99.5 % / Observed criterion σ(I): 4.4 / Redundancy: 6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 15.3
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 4.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UOC

1uoc


Resolution: 2.4→60.14 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2292 5 %
Rwork0.19 --
obs0.1923 27615 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.622 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1943 Å20 Å20 Å2
2---7.6185 Å20 Å2
3---11.8128 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3878 0 0 149 4027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073971
X-RAY DIFFRACTIONf_angle_d1.0525388
X-RAY DIFFRACTIONf_dihedral_angle_d13.8991431
X-RAY DIFFRACTIONf_chiral_restr0.072610
X-RAY DIFFRACTIONf_plane_restr0.004679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.29022300.2134347X-RAY DIFFRACTION100
2.4858-2.58530.25322280.20384347X-RAY DIFFRACTION100
2.5853-2.7030.29542260.20384300X-RAY DIFFRACTION100
2.703-2.84550.27362300.21234380X-RAY DIFFRACTION100
2.8455-3.02380.23742260.19414321X-RAY DIFFRACTION100
3.0238-3.25720.22152300.18764382X-RAY DIFFRACTION100
3.2572-3.5850.22052370.17474334X-RAY DIFFRACTION100
3.585-4.10360.21832310.17164332X-RAY DIFFRACTION100
4.1036-5.16970.2082240.16124355X-RAY DIFFRACTION100
5.1697-60.15840.23242300.20294337X-RAY DIFFRACTION100

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