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- PDB-8q1q: mouse Keap1 in complex with stapled peptide -

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Basic information

Entry
Database: PDB / ID: 8q1q
Titlemouse Keap1 in complex with stapled peptide
Components
  • Kelch-like ECH-associated protein 1
  • Stapled peptide
KeywordsLIGASE / Keap1 / cyclic peptide / E3 ligase adaptor / antioxidant response
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 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / 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-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / 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 motif / Kelch repeat type 1 / 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-IZS / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.378 Å
AuthorsKack, H. / Wissler, L.
Funding support Sweden, United Kingdom, Czech Republic, 5items
OrganizationGrant numberCountry
Swedish Research Council2018-07152 Sweden
UK Research and Innovation (UKRI) United Kingdom
Other government2019-02496 Sweden
Other government22-07138O Czech Republic
Other private22.39 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: A cell-active cyclic peptide targeting the Nrf2/Keap1 protein-protein interaction.
Authors: Iegre, J. / Krajcovicova, S. / Gunnarsson, A. / Wissler, L. / Kack, H. / Luchniak, A. / Tangefjord, S. / Narjes, F. / Spring, D.R.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,9974
Polymers34,6502
Non-polymers3472
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11 kcal/mol
Surface area12390 Å2
Unit cell
Length a, b, c (Å)103.44, 103.44, 55.675
Angle α, β, γ (deg.)90, 90, 120
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: 33305.250 Da / Num. of mol.: 1
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) / References: UniProt: Q9Z2X8
#2: Protein/peptide Stapled peptide


Mass: 1344.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IZS / ethyl 2-[(4,6-diethylpyrimidin-2-yl)-methyl-amino]ethanoate


Mass: 251.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.9
Details: 0.7-0.9M Lithium Sulfate, 0.5-0.7M Ammonium sulfate and 0.1M Sodium Citrate pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.38→89.6 Å / Num. obs: 53417 / % possible obs: 95.3 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.9
Reflection shellResolution: 1.38→1.47 Å / Rmerge(I) obs: 1.194 / Num. unique obs: 2671 / CC1/2: 0.49

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.378→19.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.968 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 2715 -RANDOM
Rwork0.1694 ---
obs0.1702 53385 76.2 %-
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8716 Å20 Å20 Å2
2---0.8716 Å20 Å2
3---1.7432 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.378→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 116 280 2609
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.143268HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d830SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it2399HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion294SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2288SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.52
X-RAY DIFFRACTIONt_other_torsion13.75
LS refinement shellResolution: 1.38→1.43 Å
RfactorNum. reflection% reflection
Rfree0.2719 51 -
Rwork0.2596 --
obs0.2602 1068 15.1 %
Refinement TLS params.Origin x: -90.5009 Å / Origin y: 101.2274 Å / Origin z: -3.3691 Å
111213212223313233
T-0.033 Å2-0.007 Å2-0.0043 Å2--0.0609 Å20.0225 Å2---0.0015 Å2
L1.7007 °20.6318 °2-0.1629 °2-1.6707 °20.1516 °2--0.6182 °2
S0.0706 Å °0.0161 Å °-0.0258 Å °0.0161 Å °-0.0367 Å °-0.0168 Å °-0.0258 Å °-0.0168 Å °-0.0339 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A325 - 612
2X-RAY DIFFRACTION1{ A|* }A1103 - 1379
3X-RAY DIFFRACTION1{ A|* }A1401

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