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- PDB-4zy3: Crystal Structure of Keap1 in Complex with a small chemical compo... -

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Basic information

Entry
Database: PDB / ID: 4zy3
TitleCrystal Structure of Keap1 in Complex with a small chemical compound, K67
ComponentsKelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / Nrf2 / Keap1 / Stress sensor / Small molecule binding / Double glycine repeat / Kelch domain / p62
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
FORMIC ACID / Chem-K67 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFukutomi, T. / Iso, T. / Suzuki, T. / Takagi, K. / Mizushima, T. / Komatsu, M. / Yamamoto, M.
CitationJournal: Nat Commun / Year: 2016
Title: p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming
Authors: Saito, T. / Ichimura, Y. / Taguchi, K. / Suzuki, T. / Mizushima, T. / Takagi, K. / Hirose, Y. / Nagahashi, M. / Iso, T. / Fukutomi, T. / Ohishi, M. / Endo, K. / Uemura, T. / Nishito, Y. / ...Authors: Saito, T. / Ichimura, Y. / Taguchi, K. / Suzuki, T. / Mizushima, T. / Takagi, K. / Hirose, Y. / Nagahashi, M. / Iso, T. / Fukutomi, T. / Ohishi, M. / Endo, K. / Uemura, T. / Nishito, Y. / Okuda, S. / Obata, M. / Kouno, T. / Imamura, R. / Tada, Y. / Obata, R. / Yasuda, D. / Takahashi, K. / Fujimura, T. / Pi, J. / Lee, M.S. / Ueno, T. / Ohe, T. / Mashino, T. / Wakai, T. / Kojima, H. / Okabe, T. / Nagano, T. / Motohashi, H. / Waguri, S. / Soga, T. / Yamamoto, M. / Tanaka, K. / Komatsu, M.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: 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
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7986
Polymers68,5402
Non-polymers1,2574
Water4,468248
1
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8993
Polymers34,2701
Non-polymers6292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-1 kcal/mol
Surface area11770 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8993
Polymers34,2701
Non-polymers6292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.399, 75.193, 109.797
Angle α, β, γ (deg.)90.00, 105.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34270.109 Da / Num. of mol.: 2 / Fragment: UNP residues 321-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl 21 Gold(de3) / References: UniProt: Q9Z2X8
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-K67 / N,N'-[2-(2-oxopropyl)naphthalene-1,4-diyl]bis(4-ethoxybenzenesulfonamide)


Mass: 582.688 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H30N2O7S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.67 Å3/Da / Density % sol: 66.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM sodium HEPES (pH 7.5), 2.0M ammonium formate, 3% (w/v) 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 92289 / % possible obs: 100 % / Redundancy: 3.6 % / Net I/σ(I): 35.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDZ

3wdz


Resolution: 1.8→33.46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.054 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21178 4623 5 %RANDOM
Rwork0.18961 ---
obs0.19072 87663 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.139 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.01 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 86 248 4712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0194576
X-RAY DIFFRACTIONr_bond_other_d0.0030.024110
X-RAY DIFFRACTIONr_angle_refined_deg2.3411.9546232
X-RAY DIFFRACTIONr_angle_other_deg1.24639388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7285568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23222.617214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31215660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0481542
X-RAY DIFFRACTIONr_chiral_restr0.1760.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215338
X-RAY DIFFRACTIONr_gen_planes_other0.010.021160
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 317 -
Rwork0.23 6349 -
obs--97.77 %

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