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- PDB-5ajd: Not1 C-terminal domain in complex with Not4 -

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Basic information

Entry
Database: PDB / ID: 5ajd
TitleNot1 C-terminal domain in complex with Not4
Components
  • CDC39P
  • GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
KeywordsTRANSCRIPTION / CCR4-NOT / NOT1 / NOT4
Function / homology
Function and homology information


response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / proteasomal protein catabolic process ...response to pheromone triggering conjugation with cellular fusion / negative regulation of cytoplasmic mRNA processing body assembly / pseudohyphal growth / deadenylation-independent decapping of nuclear-transcribed mRNA / CCR4-NOT core complex / CCR4-NOT complex / nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / ATPase activator activity / proteasomal protein catabolic process / P-body / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / negative regulation of translation / molecular adaptor activity / protein ubiquitination / regulation of cell cycle / regulation of transcription by RNA polymerase II / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #790 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #800 / RING/Ubox like zinc-binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat 1 / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / CCR4-NOT transcription complex subunit 1 HEAT repeat / CCR4-Not complex component, Not1, C-terminal / CCR4-NOT transcription complex subunit 1, domain 4 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #790 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #800 / RING/Ubox like zinc-binding domain / CCR4-NOT transcription complex subunit 1, HEAT repeat 1 / CNOT4, RNA recognition motif / NOT4, modified RING finger, HC subclass (C4C4-type) / CCR4-NOT transcription complex subunit 4 / 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 / RNA recognition motif domain, eukaryote / RNA recognition motif / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Cdc39p / General negative regulator of transcription subunit 1 / General negative regulator of transcription subunit 4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.62 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 23, 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
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDC39P
B: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
C: CDC39P
D: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
E: CDC39P
F: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
G: CDC39P
H: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
I: CDC39P
J: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
K: CDC39P
L: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)433,47512
Polymers433,47512
Non-polymers00
Water0
1
A: CDC39P
B: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CDC39P
D: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: CDC39P
H: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: CDC39P
F: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: CDC39P
J: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: CDC39P
L: GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4


Theoretical massNumber of molelcules
Total (without water)72,2462
Polymers72,2462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.658, 173.658, 262.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5166, -0.8562, -0.0089), (-0.8562, 0.5166, 0.0047), (0.0005, 0.01, -0.9999)86.996, 48.8165, -84.5882
2given(0.4911, 0.8686, -0.0655), (0.8711, -0.4897, 0.0368), (-0.0001, -0.0751, -0.9972)-5.1648, 4.4922, -87.4099
3given(0.9995, -0.0297, 0.0064), (0.0298, 0.9995, -0.0049), (-0.0062, 0.0051, 1)-85.4594, -52.6274, -3.2839
4given(-0.9978, 0.0306, 0.0587), (-0.0324, -0.9991, -0.0286), (0.0578, -0.0305, 0.9979)85.5611, 54.4064, -7.1052
5given(0.5162, 0.8546, -0.0574), (0.8565, -0.5153, 0.0298), (-0.0042, -0.0646, -0.9979)-91.8035, -44.6605, -80.3198
6given(-0.5095, -0.8605, 0.0011), (-0.8605, 0.5095, -0.0021), (0.0013, -0.002, -1)87.4044, 49.0522, -84.0615
7given(0.474, 0.8788, -0.0545), (0.8805, -0.4736, 0.0208), (-0.0075, -0.0579, -0.9983)-3.5945, 3.1164, -87.1565
8given(0.9988, -0.0495, -0.0013), (0.0495, 0.9988, 0.0064), (0.0009, -0.0065, 1)-83.9602, -54.3893, -3.1947
9given(-0.9984, 0.032, 0.0466), (-0.0323, -0.9995, -0.0067), (0.0464, -0.0082, 0.9989)85.4874, 54.8067, -6.6063
10given(0.5146, 0.8561, -0.0473), (0.8573, -0.5148, 0.0088), (-0.0169, -0.0451, -0.9988)-91.0158, -46.0522, -79.8716

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Components

#1: Protein
CDC39P / NOT1


Mass: 64811.562 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1542-2094
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: CEN.PK113-7D / Plasmid: PEC-HIS-SUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: N1P976, UniProt: P25655*PLUS
#2: Protein
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 / MODULATOR OF TRANSCRIPTION 2 / NOT4


Mass: 7434.225 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 418-477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Plasmid: PEC-HIS-GST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P34909
Sequence detailsRSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE GPDSM RESIDUES ARE LEFT OVER AFTER THE TAG CLEAVAGE

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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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growpH: 7.5
Details: 10% (W/V) PEG 4000, 0.02 M OF 1, 6-HEXANEDIOL, 0.02 M OF 1-BUTANOL, 0.02 M OF 1, 2-PROPANEDIOL (RACEMIC), 0.02 M OF 2-PROPANOL, 0T.02 M OF 1,4- BUTANEDIOL, 0.02 M OF 1,3-PROPANEDIOL, 0.1 M ...Details: 10% (W/V) PEG 4000, 0.02 M OF 1, 6-HEXANEDIOL, 0.02 M OF 1-BUTANOL, 0.02 M OF 1, 2-PROPANEDIOL (RACEMIC), 0.02 M OF 2-PROPANOL, 0T.02 M OF 1,4- BUTANEDIOL, 0.02 M OF 1,3-PROPANEDIOL, 0.1 M MOPS/HEPES-NA 7.5 AND 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2014
RadiationMonochromator: MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3.62→75.66 Å / Num. obs: 52676 / % possible obs: 99.8 % / Observed criterion σ(I): 1.3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.26
Reflection shellResolution: 3.62→3.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.37 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BY6

4by6


Resolution: 3.62→75.655 Å / SU ML: 0.65 / σ(F): 1.29 / Phase error: 40.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3187 4961 5 %
Rwork0.2662 --
obs0.2688 99916 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.62→75.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24547 0 0 0 24547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325127
X-RAY DIFFRACTIONf_angle_d0.60534345
X-RAY DIFFRACTIONf_dihedral_angle_d9.5688429
X-RAY DIFFRACTIONf_chiral_restr0.0254132
X-RAY DIFFRACTIONf_plane_restr0.0034288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6198-3.66090.38791550.39262952X-RAY DIFFRACTION93
3.6609-3.7040.46051680.38593201X-RAY DIFFRACTION100
3.704-3.74920.42661660.38433108X-RAY DIFFRACTION99
3.7492-3.79660.41451710.38873249X-RAY DIFFRACTION100
3.7966-3.84660.46731650.38693152X-RAY DIFFRACTION100
3.8466-3.89930.43561680.35923206X-RAY DIFFRACTION100
3.8993-3.9550.41691690.3663194X-RAY DIFFRACTION100
3.955-4.0140.39761630.3433176X-RAY DIFFRACTION99
4.014-4.07670.35481670.34253176X-RAY DIFFRACTION100
4.0767-4.14360.38541660.31923212X-RAY DIFFRACTION100
4.1436-4.2150.3681600.30753119X-RAY DIFFRACTION99
4.215-4.29170.36281690.31863179X-RAY DIFFRACTION99
4.2917-4.37420.34941680.31423203X-RAY DIFFRACTION99
4.3742-4.46350.34551640.30143122X-RAY DIFFRACTION99
4.4635-4.56050.33051680.29553223X-RAY DIFFRACTION99
4.5605-4.66660.38861610.26353114X-RAY DIFFRACTION100
4.6666-4.78330.3151690.26953203X-RAY DIFFRACTION99
4.7833-4.91260.29781570.26893148X-RAY DIFFRACTION99
4.9126-5.05710.33571610.27363171X-RAY DIFFRACTION99
5.0571-5.22030.3531630.27523191X-RAY DIFFRACTION99
5.2203-5.40680.32971680.28493228X-RAY DIFFRACTION100
5.4068-5.62320.32091630.2653149X-RAY DIFFRACTION99
5.6232-5.87910.31521690.27913163X-RAY DIFFRACTION100
5.8791-6.18890.39541690.27963195X-RAY DIFFRACTION100
6.1889-6.57640.37911700.27753176X-RAY DIFFRACTION100
6.5764-7.08390.33131660.26333186X-RAY DIFFRACTION100
7.0839-7.79610.30421690.25013209X-RAY DIFFRACTION100
7.7961-8.92270.261700.20173172X-RAY DIFFRACTION100
8.9227-11.23570.19781600.14633155X-RAY DIFFRACTION98
11.2357-75.67130.22991590.21723023X-RAY DIFFRACTION95

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