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- PDB-4cv5: yeast NOT1 CN9BD-CAF40 complex -

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Basic information

Entry
Database: PDB / ID: 4cv5
Titleyeast NOT1 CN9BD-CAF40 complex
Components
  • GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
  • PROTEIN CAF40
KeywordsCELL CYCLE
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 / mRNA catabolic process / ATPase activator activity / transcription elongation by RNA polymerase II / P-body ...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 / mRNA catabolic process / ATPase activator activity / transcription elongation by RNA polymerase II / P-body / 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 transcription complex subunit 9 / Cell differentiation family, Rcd1-like / 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, HEAT repeat 1 / CCR4-NOT transcription complex subunit 1 HEAT repeat / CCR4-NOT transcription complex subunit 9 / Cell differentiation family, Rcd1-like / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / General negative regulator of transcription subunit 1 / Protein CAF40
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.807 Å
AuthorsBasquin, J. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression.
Authors: Mathys, H. / Basquin, J. / Ozgur, S. / Czarnocki-Cieciura, M. / Bonneau, F. / Aartse, A. / Dziembowski, A. / Nowotny, M. / Conti, E. / Filipowicz, W.
History
DepositionMar 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references

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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: PROTEIN CAF40
C: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
D: PROTEIN CAF40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,3337
Polymers119,1994
Non-polymers6,1343
Water0
1
A: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
B: PROTEIN CAF40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7335
Polymers59,5992
Non-polymers6,1343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-21.3 kcal/mol
Surface area21540 Å2
MethodPISA
2
C: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
D: PROTEIN CAF40


Theoretical massNumber of molelcules
Total (without water)59,5992
Polymers59,5992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-21.2 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.339, 188.339, 126.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8499, 0.1547, -0.5037), (-0.1564, 0.8388, 0.5215), (0.5031, 0.522, -0.688)49.99, -52.65, 137.5
2given(-0.8465, -0.1293, 0.5164), (0.1785, 0.845, 0.5041), (-0.5015, 0.5189, -0.6923)-40.13, -33.21, 148.3

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Components

#1: Protein GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 / CELL DIVISION CYCLE PROTEIN 39 / NOT1-CN9BD


Mass: 23529.105 Da / Num. of mol.: 2 / Fragment: RESIDUES 1071-1282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288P / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P25655
#2: Protein PROTEIN CAF40 / 40 KDA CCR4-ASSOCIATED FACTOR / CAF40


Mass: 36070.375 Da / Num. of mol.: 2 / Fragment: RESIDUES 54-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288P / Plasmid: PEC_HIS_SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): GOLD / References: UniProt: P53829
#3: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br12Ta6

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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: 4.7 Å3/Da / Density % sol: 74 % / Description: NONE
Crystal growpH: 7 / Details: 50 MM HEPES PH 7.0, 3 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.25472
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25472 Å / Relative weight: 1
ReflectionResolution: 3.81→48.29 Å / Num. obs: 22861 / % possible obs: 99.8 % / Observed criterion σ(I): 2.7 / Redundancy: 25.5 % / Biso Wilson estimate: 147.65 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 18
Reflection shellResolution: 3.81→4.01 Å / Redundancy: 23.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.807→48.292 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 37.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2952 2122 5 %
Rwork0.2764 --
obs0.2773 22828 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.807→48.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6118 0 54 0 6172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036204
X-RAY DIFFRACTIONf_angle_d0.8858498
X-RAY DIFFRACTIONf_dihedral_angle_d12.7552019
X-RAY DIFFRACTIONf_chiral_restr0.0631116
X-RAY DIFFRACTIONf_plane_restr0.0041072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8075-3.8960.49011380.42892629X-RAY DIFFRACTION97
3.896-3.99340.41731430.37232716X-RAY DIFFRACTION100
3.9934-4.10130.36741420.3442689X-RAY DIFFRACTION100
4.1013-4.22190.33811400.31232690X-RAY DIFFRACTION100
4.2219-4.35810.31751390.29562689X-RAY DIFFRACTION100
4.3581-4.51380.33721430.28632706X-RAY DIFFRACTION100
4.5138-4.69440.33591430.27242682X-RAY DIFFRACTION100
4.6944-4.90780.29151420.25222700X-RAY DIFFRACTION100
4.9078-5.16630.32071450.27582706X-RAY DIFFRACTION100
5.1663-5.48960.2651400.28362675X-RAY DIFFRACTION100
5.4896-5.91270.37591420.33032710X-RAY DIFFRACTION100
5.9127-6.50650.40531410.32022704X-RAY DIFFRACTION100
6.5065-7.4450.38481400.30712704X-RAY DIFFRACTION100
7.445-9.36870.20321400.22252699X-RAY DIFFRACTION100
9.3687-48.29580.22471440.23742695X-RAY DIFFRACTION100

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