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- PDB-7eca: Crystal structure of the Keap1 complex with a peptide base on ETG... -

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Basic information

Entry
Database: PDB / ID: 7eca
TitleCrystal structure of the Keap1 complex with a peptide base on ETGE motif.
Components
  • Kelch-like ECH-associated protein 1
  • LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO
KeywordsCYTOSOLIC PROTEIN / Nrf2 / Oxidative stress / cancer
Function / homology
Function and homology information


aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / regulation of epidermal cell differentiation / Neddylation ...aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / Nuclear events mediated by NFE2L2 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of cellular response to hypoxia / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / regulation of epidermal cell differentiation / Neddylation / cellular response to laminar fluid shear stress / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / cellular response to fluid shear stress / cellular response to methionine / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / negative regulation of ferroptosis / negative regulation of cardiac muscle cell apoptotic process / proteasomal ubiquitin-independent protein catabolic process / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / transcription regulator inhibitor activity / transcription factor binding / negative regulation of vascular associated smooth muscle cell migration / regulation of embryonic development / centriolar satellite / cellular response to angiotensin / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / ubiquitin-like ligase-substrate adaptor activity / negative regulation of endothelial cell apoptotic process / cellular response to glucose starvation / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / inclusion body / cellular response to copper ion / response to endoplasmic reticulum stress / reactive oxygen species metabolic process / cellular response to interleukin-4 / cell redox homeostasis / transcription coregulator binding / response to ischemia / regulation of autophagy / actin filament / positive regulation of D-glucose import / protein-DNA complex / molecular condensate scaffold activity / positive regulation of neuron projection development / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / disordered domain specific binding / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / midbody / ubiquitin-dependent protein catabolic process / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / sequence-specific DNA binding / transcription cis-regulatory region binding / protein ubiquitination / inflammatory response / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / Kelch-like ECH-associated protein 1 / : / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch ...: / Basic leucine zipper domain, Maf-type / bZIP Maf transcription factor / Transcription factor, Skn-1-like, DNA-binding domain superfamily / 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 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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
Nuclear factor erythroid 2-related factor 2 / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.00006351943 Å
AuthorsCheng, L. / Wang, C.
CitationJournal: Life Sci / Year: 2021
Title: New insights into the mechanism of Keap1-Nrf2 interaction based on cancer-associated mutations.
Authors: Cheng, L. / Wang, H. / Li, S. / Liu, Z. / Wang, C.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,82113
Polymers39,7642
Non-polymers1,05711
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-148 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.814, 102.814, 54.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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


Mass: 36850.270 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 LEU-ASP-GLU-GLU-THR-GLY-GLU-PHE-LEU-PRO


Mass: 2914.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q60795
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Lithium Sulfate,Ammonium Sulfate,sodium citrate 5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→20.135 Å / Num. obs: 22476 / % possible obs: 99.83 % / Redundancy: 8.4 % / Biso Wilson estimate: 20.3899710197 Å2 / CC1/2: 0.996 / Net I/σ(I): 1.96
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 164132 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
CrysalisPro1.171.40.54adata reduction
CCP47.0.053data scaling
CCP47.0.053phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1x2r

1x2r


Resolution: 2.00006351943→20.1349848749 Å / SU ML: 0.237795283374 / Cross valid method: FREE R-VALUE / σ(F): 1.35299871149 / Phase error: 25.3838261616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235456817831 1147 5.10526550051 %
Rwork0.196822366979 21320 -
obs0.198818141711 22467 99.9466168424 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.6687614344 Å2
Refinement stepCycle: LAST / Resolution: 2.00006351943→20.1349848749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 55 160 2515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002379120852572400
X-RAY DIFFRACTIONf_angle_d0.5773137651913273
X-RAY DIFFRACTIONf_chiral_restr0.0473419261539342
X-RAY DIFFRACTIONf_plane_restr0.00395850771617424
X-RAY DIFFRACTIONf_dihedral_angle_d5.825473150271364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.0910.30547494461450.273893598772657X-RAY DIFFRACTION99.8218738867
2.091-2.20110.2892402960421430.2274109854362643X-RAY DIFFRACTION99.9641191245
2.2011-2.33880.3022365909061240.2410544941092653X-RAY DIFFRACTION99.9280316661
2.3388-2.51910.2946799726781310.2229791234442674X-RAY DIFFRACTION99.9643620813
2.5191-2.7720.2716085925911570.2153108903282644X-RAY DIFFRACTION100
2.772-3.17180.2441185882031460.1968067796262647X-RAY DIFFRACTION100
3.1718-3.9910.1945233823761510.161425567062674X-RAY DIFFRACTION100
3.991-6.640.1808859169741500.1671297174922728X-RAY DIFFRACTION99.9305555556

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