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- PDB-4b8c: nuclease module of the yeast Ccr4-Not complex -

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Basic information

Entry
Database: PDB / ID: 4b8c
Titlenuclease module of the yeast Ccr4-Not complex
Components
  • GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
  • GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
  • POLY(A) RIBONUCLEASE POP2
KeywordsHYDROLASE/CELL CYCLE / HYDROLASE-CELL CYCLE 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 / CCR4-NOT complex / Cdc73/Paf1 complex / : ...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 / CCR4-NOT complex / Cdc73/Paf1 complex / : / nuclear-transcribed mRNA poly(A) tail shortening / traversing start control point of mitotic cell cycle / DNA replication checkpoint signaling / 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 / DNA replication / molecular adaptor activity / regulation of cell cycle / regulation of transcription by RNA polymerase II / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #190 / HIV-1 Nucleocapsid Protein - #20 / 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 ...Ribosomal Protein S8; Chain: A, domain 1 - #190 / HIV-1 Nucleocapsid Protein - #20 / 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 / HIV-1 Nucleocapsid Protein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Ribosomal Protein S8; Chain: A, domain 1 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Endonuclease/exonuclease/phosphatase superfamily / Alpha-Beta Horseshoe / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Ribonuclease H-like superfamily/Ribonuclease H / Leucine-rich repeat domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Few Secondary Structures / Irregular / 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 / CCR4-Not complex 3'-5'-exoribonuclease subunit Ccr4 / Poly(A) ribonuclease POP2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SACCHAROMYCES CEREVISIAE S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 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 1.1Jan 1, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLY(A) RIBONUCLEASE POP2
B: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
C: POLY(A) RIBONUCLEASE POP2
D: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
E: POLY(A) RIBONUCLEASE POP2
F: POLY(A) RIBONUCLEASE POP2
G: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
H: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
I: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
J: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
K: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
L: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR


Theoretical massNumber of molelcules
Total (without water)579,03512
Polymers579,03512
Non-polymers00
Water0
1
A: POLY(A) RIBONUCLEASE POP2
B: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
D: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
F: POLY(A) RIBONUCLEASE POP2

G: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
J: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR


Theoretical massNumber of molelcules
Total (without water)289,5176
Polymers289,5176
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area10730 Å2
ΔGint-50 kcal/mol
Surface area65190 Å2
MethodPISA
2
C: POLY(A) RIBONUCLEASE POP2
E: POLY(A) RIBONUCLEASE POP2
H: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
K: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR
L: GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR

I: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1


Theoretical massNumber of molelcules
Total (without water)289,5176
Polymers289,5176
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area10670 Å2
ΔGint-49 kcal/mol
Surface area65420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.650, 122.911, 126.421
Angle α, β, γ (deg.)89.47, 89.74, 64.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
32
42
13
23
33
43
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN K AND (RESSEQ 134:143 OR RESSEQ 145:187 OR RESSEQ...
211CHAIN D AND (RESSEQ 134:143 OR RESSEQ 145:187 OR RESSEQ...
112CHAIN C AND (RESSEQ 149:356 OR RESSEQ 370:428 )
212CHAIN A AND (RESSEQ 149:356 OR RESSEQ 370:428 )
312CHAIN E AND (RESSEQ 149:356 OR RESSEQ 370:428 )
412CHAIN F AND (RESSEQ 149:356 OR RESSEQ 370:428 )
113CHAIN H AND (RESSEQ 759:991 )
213CHAIN B AND (RESSEQ 759:991 )
313CHAIN G AND (RESSEQ 759:991 )
413CHAIN I AND (RESSEQ 759:991 )
114CHAIN J AND (RESSEQ 134:143 OR RESSEQ 145:187 OR RESSEQ 242:261 OR RESSEQ 332:468 )
214CHAIN L AND (RESSEQ 134:143 OR RESSEQ 145:187 OR RESSEQ 242:261 OR RESSEQ 332:468 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
POLY(A) RIBONUCLEASE POP2 / POP2 / CCR4-ASSOCIATED FACTOR 1


Mass: 33303.543 Da / Num. of mol.: 4 / Fragment: NUCLEASE DOMAIN, RESIDUES 146-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PFAST BAC DUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P39008, poly(A)-specific ribonuclease
#2: Protein
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 / NOT1 / CELL DIVISION CYCLE PROTEIN 39


Mass: 28527.402 Da / Num. of mol.: 4 / 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 / Variant (production host): PLYS.STAR / References: UniProt: P25655
#3: Protein
GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR / CCR4 / CARBON CATABOLITE REPRESSOR PROTEIN 4 / CYTOPLASMIC DEADENYLASE


Mass: 82927.688 Da / Num. of mol.: 4 / Fragment: LLR-NUCLEASE, RESIDUES 111-837
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE S288C (yeast) / Plasmid: PFAST BAC DUAL / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SSF9 / References: UniProt: P31384, poly(A)-specific ribonuclease

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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: 2.93 Å3/Da / Density % sol: 58.1 % / Description: NONE
Crystal growpH: 7.5
Details: 8% PEG 3350, 75 MM AMMONIUM ACETATE AND 10% GLYCEROL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.22 Å / Num. obs: 90023 / % possible obs: 98.5 % / Observed criterion σ(I): 2.8 / Redundancy: 3.6 % / Biso Wilson estimate: 78.43 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 11.2
Reflection shellResolution: 3.4→3.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B8A

4b8a


Resolution: 3.41→47.951 Å / SU ML: 1.07 / σ(F): 1.99 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 8794 5 %
Rwork0.2333 --
obs0.2351 90023 97.11 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.119 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.9146 Å29.5422 Å23.0339 Å2
2--12.7405 Å20.1461 Å2
3----2.8259 Å2
Refinement stepCycle: LAST / Resolution: 3.41→47.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24298 0 0 0 24298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124915
X-RAY DIFFRACTIONf_angle_d1.46833880
X-RAY DIFFRACTIONf_dihedral_angle_d17.0698898
X-RAY DIFFRACTIONf_chiral_restr0.1053850
X-RAY DIFFRACTIONf_plane_restr0.0064294
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11K2361X-RAY DIFFRACTIONPOSITIONAL
12D2361X-RAY DIFFRACTIONPOSITIONAL0.061
21C2170X-RAY DIFFRACTIONPOSITIONAL
22A2170X-RAY DIFFRACTIONPOSITIONAL0.035
23E2170X-RAY DIFFRACTIONPOSITIONAL0.069
24F2170X-RAY DIFFRACTIONPOSITIONAL0.07
31H1869X-RAY DIFFRACTIONPOSITIONAL
32B1869X-RAY DIFFRACTIONPOSITIONAL0.029
33G1869X-RAY DIFFRACTIONPOSITIONAL0.044
34I1869X-RAY DIFFRACTIONPOSITIONAL0.042
41J1606X-RAY DIFFRACTIONPOSITIONAL
42L1606X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.41-3.44870.36212890.33165497X-RAY DIFFRACTION97
3.4487-3.48930.32232910.28395589X-RAY DIFFRACTION97
3.4893-3.53180.29462910.29175531X-RAY DIFFRACTION97
3.5318-3.57650.36372890.28585543X-RAY DIFFRACTION97
3.5765-3.62360.29542980.26545648X-RAY DIFFRACTION97
3.6236-3.67320.26492850.24695458X-RAY DIFFRACTION97
3.6732-3.72570.29552980.23915694X-RAY DIFFRACTION97
3.7257-3.78130.2612880.22935484X-RAY DIFFRACTION97
3.7813-3.84030.27073040.23415766X-RAY DIFFRACTION97
3.8403-3.90320.26372860.22475413X-RAY DIFFRACTION98
3.9032-3.97050.24582980.22065709X-RAY DIFFRACTION97
3.9705-4.04270.25132940.20235493X-RAY DIFFRACTION97
4.0427-4.12040.24412930.20245589X-RAY DIFFRACTION97
4.1204-4.20450.23122950.19625632X-RAY DIFFRACTION97
4.2045-4.29580.26972930.20485532X-RAY DIFFRACTION97
4.2958-4.39570.24743000.19915640X-RAY DIFFRACTION97
4.3957-4.50550.26512950.19955603X-RAY DIFFRACTION97
4.5055-4.62730.23512870.19075545X-RAY DIFFRACTION97
4.6273-4.76330.23692980.19375608X-RAY DIFFRACTION98
4.7633-4.91690.2192980.19115663X-RAY DIFFRACTION98
4.9169-5.09240.22292890.19195539X-RAY DIFFRACTION97
5.0924-5.29610.22892950.19985558X-RAY DIFFRACTION97
5.2961-5.53680.25692960.21325597X-RAY DIFFRACTION97
5.5368-5.82820.33942970.26595544X-RAY DIFFRACTION97
5.8282-6.19270.33482900.26965521X-RAY DIFFRACTION97
6.1927-6.66970.26922880.23915539X-RAY DIFFRACTION97
6.6697-7.33870.25672950.22635621X-RAY DIFFRACTION97
7.3387-8.39570.24292920.23475538X-RAY DIFFRACTION97
8.3957-10.55910.27932890.245513X-RAY DIFFRACTION96
10.5591-47.95580.31762930.31485534X-RAY DIFFRACTION96

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