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- PDB-5cgj: Crystal structure of murine Keap1 in complex with RA839, a non-co... -

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Basic information

Entry
Database: PDB / ID: 5cgj
TitleCrystal structure of murine Keap1 in complex with RA839, a non-covalent small-molecule binder to Keap1 and selective activator of Nrf2 signalling.
ComponentsKelch-like ECH-associated protein 1
KeywordsPROTEIN BINDING / BETA PROPELLER / Inhibitor / Complex
Function / homology
Function and homology information


cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / negative regulation of gene expression / focal adhesion / regulation of DNA-templated transcription / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif ...Kelch-type beta propeller / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-51M / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / molecular replacement / Resolution: 3.36 Å
AuthorsSchimanski-Breves, S. / Loenze, P. / Engel, C.K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterization of RA839, a Noncovalent Small Molecule Binder to Keap1 and Selective Activator of Nrf2 Signaling.
Authors: Winkel, A.F. / Engel, C.K. / Margerie, D. / Kannt, A. / Szillat, H. / Glombik, H. / Kallus, C. / Ruf, S. / Gussregen, S. / Riedel, J. / Herling, A.W. / von Knethen, A. / Weigert, A. / Brune, B. / Schmoll, D.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8656
Polymers37,0281
Non-polymers8375
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-58 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.410, 103.410, 56.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2


Mass: 37028.371 Da / Num. of mol.: 1 / Fragment: KEAP1-DC, RESIDUES 309-624
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Plasmid: PET16 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Z2X8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-51M / (3S)-1-(4-{[(2,3,5,6-tetramethylphenyl)sulfonyl]amino}naphthalen-1-yl)pyrrolidine-3-carboxylic acid


Mass: 452.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H28N2O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: AMMONIUM SULFATE 0.5M, LITHIUM SULFATE 0.9M, SODIUM CITRATE 0.1M, PH 5.5, VAPOR DIFFUSION, SITTING DROP,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.6→51.73 Å / Num. all: 5029 / Num. obs: 5014 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.06 / Rrim(I) all: 0.191 / Rsym value: 0.172 / Net I/av σ(I): 4.222 / Net I/σ(I): 12.8 / Num. measured all: 50822
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 13.5 / Num. measured all: 1532 / Num. unique all: 174 / Rpim(I) all: 0.017 / Rsym value: 0.046 / Net I/σ(I) obs: 35.4 / Rejects: 0 / % possible all: 68.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.20data scaling
PHASERphasing
BUSTER-TNTBUSTER 2.11.2refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MIR / Resolution: 3.36→51.71 Å / Cor.coef. Fo:Fc: 0.9045 / Cor.coef. Fo:Fc free: 0.8464 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.501
RfactorNum. reflection% reflectionSelection details
Rfree0.226 254 5.07 %RANDOM
Rwork0.1367 ---
obs0.141 5014 99.94 %-
Displacement parametersBiso max: 122.91 Å2 / Biso mean: 49.53 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-14.8919 Å20 Å20 Å2
2--14.8919 Å20 Å2
3----29.7838 Å2
Refine analyzeLuzzati coordinate error obs: 0.445 Å
Refinement stepCycle: final / Resolution: 3.36→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 52 12 2290
Biso mean--74.12 15.33 -
Num. residues----290
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d765SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes350HARMONIC5
X-RAY DIFFRACTIONt_it2336HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion283SEMIHARMONIC5
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_contact2746SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2336HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg3188HARMONIC21.27
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion21.43
LS refinement shellResolution: 3.36→3.76 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2456 83 5.91 %
Rwork0.1359 1322 -
all0.1423 1405 -
obs--99.94 %

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