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- PDB-5x54: Crystal structure of the Keap1 Kelch domain in complex with a tet... -

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Basic information

Entry
Database: PDB / ID: 5x54
TitleCrystal structure of the Keap1 Kelch domain in complex with a tetrapeptide
Components
  • ACE-GLU-TRP-TRP-TRP
  • Kelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / Transcription / Complex / Inhibitor / Kelch domain / NRF2 / Oxidative stress / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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-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
ACETATE ION / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSogabe, S. / Kadotani, A. / Lane, W. / Snell, G.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Discovery of a Kelch-like ECH-associated protein 1-inhibitory tetrapeptide and its structural characterization
Authors: Sogabe, S. / Sakamoto, K. / Kamada, Y. / Kadotani, A. / Fukuda, Y. / Sakamoto, J.
History
DepositionFeb 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Nov 22, 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
C: ACE-GLU-TRP-TRP-TRP
D: ACE-GLU-TRP-TRP-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1796
Polymers65,0614
Non-polymers1182
Water5,729318
1
A: Kelch-like ECH-associated protein 1
C: ACE-GLU-TRP-TRP-TRP


Theoretical massNumber of molelcules
Total (without water)32,5302
Polymers32,5302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-4 kcal/mol
Surface area11850 Å2
MethodPISA
2
B: Kelch-like ECH-associated protein 1
D: ACE-GLU-TRP-TRP-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6484
Polymers32,5302
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.566, 75.705, 168.132
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 Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31798.502 Da / Num. of mol.: 2 / Fragment: UNP residues 321-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide ACE-GLU-TRP-TRP-TRP


Mass: 731.796 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage T7 (virus)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: bis-tris, sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976486 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976486 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39255 / % possible obs: 98.7 % / Redundancy: 7.2 % / CC1/2: 0.996 / Rpim(I) all: 0.06 / Rsym value: 0.15 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 3.1 / CC1/2: 0.846 / Rpim(I) all: 0.283 / Rsym value: 0.666 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U6D

1u6d


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.375 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.176 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20808 1957 5 %RANDOM
Rwork0.16734 ---
obs0.16933 37219 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0 Å20 Å2
2--1.34 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 8 318 4824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194620
X-RAY DIFFRACTIONr_bond_other_d0.0020.024032
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.936294
X-RAY DIFFRACTIONr_angle_other_deg0.97939286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2065574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21922.434226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215324
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021048
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_it0.7911.9812314
X-RAY DIFFRACTIONr_mcbond_other0.791.982311
X-RAY DIFFRACTIONr_mcangle_it1.3942.9662882
X-RAY DIFFRACTIONr_mcangle_other1.3942.9662883
X-RAY DIFFRACTIONr_scbond_it1.0362.1442306
X-RAY DIFFRACTIONr_scbond_other1.0352.1442307
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7833.1653415
X-RAY DIFFRACTIONr_long_range_B_refined3.07522.4974980
X-RAY DIFFRACTIONr_long_range_B_other3.01522.3264935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 162 -
Rwork0.23 2722 -
obs--100 %
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)
11.0280.03960.32710.2360.10810.4076-0.0147-0.02380.0367-0.04030.0293-0.0171-0.01130.0306-0.01460.0077-0.00590.00390.076-0.03920.02350.115318.9365-12.0129
20.71340.18750.36510.78160.09210.42480.0242-0.0043-0.00620.0284-0.02140.00140.0173-0.0081-0.00270.0133-0.00840.00850.0425-0.02610.017734.03842.9332-29.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A325 - 609
2X-RAY DIFFRACTION1C0 - 4
3X-RAY DIFFRACTION2B325 - 609
4X-RAY DIFFRACTION2D0 - 4

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