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- PDB-6ffm: Crystal Structure of Human KEAP1 BTB Domain in Complex with isoxa... -

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Basic information

Entry
Database: PDB / ID: 6ffm
TitleCrystal Structure of Human KEAP1 BTB Domain in Complex with isoxazoline-based inhibitor
ComponentsKelch-like ECH-associated protein 1
KeywordsSIGNALING PROTEIN / 3-bromo-4 5-dihydroisoxazole / BTB domain / antioxidant response
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 / negative regulation of DNA-binding transcription factor activity ...regulation of epidermal cell differentiation / Nuclear events mediated by NFE2L2 / 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 / negative regulation of DNA-binding transcription factor activity / KEAP1-NFE2L2 pathway / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to oxidative stress / Neddylation / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / protein ubiquitination / Ub-specific processing proteases / endoplasmic reticulum / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Chem-D8N / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMoniot, S. / Steegborn, C.
CitationJournal: ChemistryOpen / Year: 2018
Title: Effects of 3-Bromo-4,5-dihydroisoxazole Derivatives on Nrf2 Activation and Heme Oxygenase-1 Expression.
Authors: Pinto, A. / El Ali, Z. / Moniot, S. / Tamborini, L. / Steegborn, C. / Foresti, R. / De Micheli, C.
History
DepositionJan 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)15,4112
Polymers15,2071
Non-polymers2041
Water32418
1
A: Kelch-like ECH-associated protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)30,8224
Polymers30,4132
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area4070 Å2
ΔGint-37 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.491, 42.491, 265.213
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 Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 15206.571 Da / Num. of mol.: 1 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Plasmid: pET19mod
Details (production host): N-term His-tag cleavable with TEV protease
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14145
#2: Chemical ChemComp-D8N / ~{N}-[4-[(5~{R})-4,5-dihydro-1,2-oxazol-5-yl]phenyl]ethanamide


Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25-28 % PEG 4000, 0.1 M Tris-HCl pH 8.0 and 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2016
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91814 Å / Relative weight: 1
ReflectionResolution: 2.2→44.202 Å / Num. obs: 7968 / % possible obs: 98.73 % / Redundancy: 5.9 % / Biso Wilson estimate: 50.25 Å2 / CC1/2: 1 / Rrim(I) all: 0.1492 / Net I/σ(I): 9.33
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.57 / Num. unique obs: 752 / CC1/2: 0.33 / Rrim(I) all: 3.161 / % possible all: 99.08

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cxi

4cxi


Resolution: 2.2→44.202 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / Phase error: 37.61
RfactorNum. reflection% reflection
Rfree0.2929 793 9.98 %
Rwork0.2525 --
obs0.2568 7948 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 15 18 1053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021091
X-RAY DIFFRACTIONf_angle_d0.3981478
X-RAY DIFFRACTIONf_dihedral_angle_d10.583664
X-RAY DIFFRACTIONf_chiral_restr0.039168
X-RAY DIFFRACTIONf_plane_restr0.002192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33780.44411270.40631148X-RAY DIFFRACTION99
2.3378-2.51830.37591250.37261136X-RAY DIFFRACTION98
2.5183-2.77170.35731280.33551159X-RAY DIFFRACTION100
2.7717-3.17270.35591310.28891178X-RAY DIFFRACTION99
3.1727-3.99690.2971340.23371204X-RAY DIFFRACTION99
3.9969-44.21110.23941480.20681330X-RAY DIFFRACTION98
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)
13.841-3.09040.02146.05950.20212.42751.05960.67480.3873-0.5398-0.6391-0.66580.18960.4715-0.19150.58820.0781-0.06160.63110.00030.578918.7508-16.609-27.7593
22.7298-1.48011.56581.8474-0.09942.57390.0083-0.2215-0.21560.4932-0.16370.46970.15170.06320.12760.51830.10670.06630.3855-0.07490.577-0.3245-13.0957-15.7097
30.28720.06030.34210.01130.0710.4056-0.0186-0.9723-0.6905-0.3516-0.33470.6521.7871-0.43910.11672.09840.1277-0.27240.90790.08061.2551-2.2405-26.8647-15.1197
45.9449-1.6046-0.45373.40361.55844.8844-0.4686-0.50990.98540.2590.33110.1073-1.2095-0.37550.06590.77440.1956-0.02750.48810.00210.52633.6584-4.1604-13.2552
55.38693.03570.56276.08891.62684.4629-0.0205-0.14550.0829-0.8055-0.0041-0.2281-0.25760.45030.04760.88680.0516-0.06450.4355-0.03140.505612.056-1.0122-4.5131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 120 )
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 180 )

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