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- PDB-4c0f: Structure of the NOT-box domain of human CNOT2 -

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Basic information

Entry
Database: PDB / ID: 4c0f
TitleStructure of the NOT-box domain of human CNOT2
ComponentsCCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION
Function / homology
Function and homology information


positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / Deadenylation of mRNA / trophectodermal cell differentiation / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors ...positive regulation of cytoplasmic mRNA processing body assembly / CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of intracellular estrogen receptor signaling pathway / Deadenylation of mRNA / trophectodermal cell differentiation / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / transcription corepressor binding / transcription coregulator activity / P-body / regulation of translation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CCR4-NOT complex subunit 2/3/5, C-terminal domain / NOT2/NOT3/NOT5, C-terminal / CCR4-NOT complex subunit 2/3/5, C-terminal domain superfamily / Not2/Not3/Not5 / NOT2/NOT3/NOT5 C-terminal / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CCR4-NOT transcription complex subunit 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBoland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Izaurralde, E. / Weichenrieder, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure and Assembly of the not Module of the Human Ccr4-not Complex
Authors: Boland, A. / Chen, Y. / Raisch, T. / Jonas, S. / Kuzuoglu-Ozturk, D. / Wohlbold, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionAug 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Atomic model / Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Nov 20, 2013Group: Database references
Revision 1.4Oct 18, 2017Group: Data collection / Category: diffrn / diffrn_source
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED THE SHEET STRUCTURES OF CHAIN A, B, C, D ARE ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED THE SHEET STRUCTURES OF CHAIN A, B, C, D ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS A, B, C, D.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)56,3924
Polymers56,3924
Non-polymers00
Water1,838102
1
A: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
B: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)28,1962
Polymers28,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-40.7 kcal/mol
Surface area15500 Å2
MethodPISA
2
C: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
D: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2


Theoretical massNumber of molelcules
Total (without water)28,1962
Polymers28,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-39.4 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.830, 64.830, 412.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 / CCR4-ASSOCIATED FACTOR 2 / CNOT2


Mass: 14097.985 Da / Num. of mol.: 4 / Fragment: NOT-BOX DOMAIN, RESIDUES 429-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9NZN8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FOUR N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.

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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: 2.7 Å3/Da / Density % sol: 54.4 %
Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97945 A, PEAK DATA AT THE SE EDGE.
Crystal growpH: 5.6
Details: 100MM TRI-SODIUM CITRATE PH=5.6, 10% PEG4000, 10% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001,0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2011 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.000011
20.979451
ReflectionResolution: 2.4→49.3 Å / Num. obs: 21312 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 43.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.8 / % possible all: 99.1

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→49.304 Å / SU ML: 0.32 / σ(F): 2 / Phase error: 26.05 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 453, 473, 490. CHAIN B, RESIDUES 424, 438, 496. CHAIN C, ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUES 453, 473, 490. CHAIN B, RESIDUES 424, 438, 496. CHAIN C, RESIDUES 430, 513. CHAIN D, RESIDUES 486, 490. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 429 TO 432 AND 529 TO 540. CHAIN B, RESIDUES 527 TO 540. CHAIN C, RESIDUES 537 TO 540. CHAIN D, RESIDUES 429 TO 440.
RfactorNum. reflection% reflection
Rfree0.2628 1066 5 %
Rwork0.217 --
obs0.2193 21287 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.58 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.6612 Å20 Å20 Å2
2--9.6612 Å20 Å2
3----19.3224 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3483 0 0 102 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023596
X-RAY DIFFRACTIONf_angle_d0.6414876
X-RAY DIFFRACTIONf_dihedral_angle_d11.6881305
X-RAY DIFFRACTIONf_chiral_restr0.043480
X-RAY DIFFRACTIONf_plane_restr0.002626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.30781280.282421X-RAY DIFFRACTION99
2.5092-2.64150.3931280.27332429X-RAY DIFFRACTION99
2.6415-2.8070.34991310.27172485X-RAY DIFFRACTION99
2.807-3.02370.33221290.24652454X-RAY DIFFRACTION99
3.0237-3.32790.24461320.2212497X-RAY DIFFRACTION99
3.3279-3.80930.23591330.20312540X-RAY DIFFRACTION99
3.8093-4.79870.22171350.17882579X-RAY DIFFRACTION100
4.7987-49.31480.25241500.21622816X-RAY DIFFRACTION100

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