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- PDB-6h3z: Crystal structure of a C-terminal MIF4G domain in NOT1 -

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Basic information

Entry
Database: PDB / ID: 6h3z
TitleCrystal structure of a C-terminal MIF4G domain in NOT1
ComponentsCCR4-not transcription complex subunit 1
KeywordsGENE REGULATION / DEADENYLATION / MRNA DECAY / CCR4-NOT / HYDROLASE / TRANSCRIPTION
Function / homology
Function and homology information


CCR4-NOT core complex / negative regulation of translation / nucleus
Similarity search - Function
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 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
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsRaisch, T. / Sandmeir, F. / Weichenrieder, O. / Valkov, E. / Izaurralde, E.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structural and biochemical analysis of a NOT1 MIF4G-like domain of the CCR4-NOT complex.
Authors: Raisch, T. / Sandmeir, F. / Weichenrieder, O. / Valkov, E. / Izaurralde, E.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CCR4-not transcription complex subunit 1
B: CCR4-not transcription complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7904
Polymers50,7442
Non-polymers462
Water0
1
A: CCR4-not transcription complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3952
Polymers25,3721
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CCR4-not transcription complex subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3952
Polymers25,3721
Non-polymers231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.930, 79.770, 98.420
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 CCR4-not transcription complex subunit 1


Mass: 25372.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first six residues (GPHMLE) stem from the plasmid backbone.
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0042750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SAL9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES/NaOH pH 7.5, 1.0 M Ammonium Sulfate, 1.0 M Potassium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03849 Å / Relative weight: 1
ReflectionResolution: 3→62 Å / Num. obs: 12140 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 121.2 Å2 / CC1/2: 1 / Rsym value: 0.061 / Net I/σ(I): 18.4
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 1.3 / CC1/2: 0.57 / Rsym value: 1.27

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.49 Å / Cor.coef. Fo:Fc: 0.9618 / Cor.coef. Fo:Fc free: 0.9313 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.375
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 603 4.98 %RANDOM
Rwork0.1824 ---
obs0.1854 12119 99.88 %-
Displacement parametersBiso mean: 110.21 Å2
Baniso -1Baniso -2Baniso -3
1--12.4654 Å20 Å20 Å2
2--2.5358 Å20 Å2
3---9.9296 Å2
Refinement stepCycle: 1 / Resolution: 3→47.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 2 0 3306
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013362HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.144567HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1197SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes104HARMONIC2
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it3362HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion452SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4037SEMIHARMONIC4
LS refinement shellResolution: 3→3.29 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3382 134 4.76 %
Rwork0.2535 2682 -
all0.2578 2816 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.04471.42151.27055.24150.65843.21460.3481-0.248-0.0173-0.0425-0.16610.3870.5584-0.3361-0.182-0.2297-0.0711-0.0893-0.10850.1202-0.2547-18.9274.463112.2741
22.537-0.5409-1.4941.31480.60815.11180.3314-0.22790.3916-0.2349-0.05480.1783-0.19160.3405-0.2766-0.1892-0.0360.0561-0.2020.05380.0238-0.0085-8.33834.9364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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