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- PDB-6t7v: KEAP1 IN COMPLEX WITH PEPTIDE 8 -

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Basic information

Entry
Database: PDB / ID: 6t7v
TitleKEAP1 IN COMPLEX WITH PEPTIDE 8
Components
  • Kelch-like ECH-associated protein 1
  • LEU-ASP-PRO-GLU-THR-GLY-GLU-PHE-LEU
KeywordsTRANSCRIPTION / KEAP1 / UBIQUITINYLATION / INRF2 / KIAA0132 / KLHL19 / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of removal of superoxide radicals ...aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of removal of superoxide radicals / regulation of cellular response to oxidative stress / regulation of epidermal cell differentiation / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / mediator complex / cellular response to methionine / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / positive regulation of ubiquitin-dependent protein catabolic process / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of response to oxidative stress / negative regulation of ferroptosis / negative regulation of cardiac muscle cell apoptotic process / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / proteasomal ubiquitin-independent protein catabolic process / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / negative regulation of vascular associated smooth muscle cell migration / regulation of embryonic development / 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 / transcription regulator inhibitor activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to glucose starvation / inclusion body / cellular response to copper ion / reactive oxygen species metabolic process / cellular response to interleukin-4 / cell redox homeostasis / transcription coregulator binding / response to ischemia / positive regulation of D-glucose import / actin filament / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / molecular condensate scaffold activity / protein-DNA complex / positive regulation of neuron projection development / centriolar satellite / 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 / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of autophagy / Ub-specific processing proteases / protein ubiquitination / ciliary basal body / 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 transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding
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 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / 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 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / 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
ACETATE ION / Kelch-like ECH-associated protein 1 / Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsColarusso, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2020
Title: Optimization of linear and cyclic peptide inhibitors of KEAP1-NRF2 protein-protein interaction.
Authors: Colarusso, S. / De Simone, D. / Frattarelli, T. / Andreini, M. / Cerretani, M. / Missineo, A. / Moretti, D. / Tambone, S. / Kempf, G. / Augustin, M. / Steinbacher, S. / Munoz-Sanjuan, I. / ...Authors: Colarusso, S. / De Simone, D. / Frattarelli, T. / Andreini, M. / Cerretani, M. / Missineo, A. / Moretti, D. / Tambone, S. / Kempf, G. / Augustin, M. / Steinbacher, S. / Munoz-Sanjuan, I. / Park, L. / Summa, V. / Tomei, L. / Bresciani, A. / Dominguez, C. / Toledo-Sherman, L. / Bianchi, E.
History
DepositionOct 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
I: LEU-ASP-PRO-GLU-THR-GLY-GLU-PHE-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0313
Polymers32,9722
Non-polymers591
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-0 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.430, 75.430, 114.497
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2 / Kelch-like protein 19


Mass: 31951.773 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, 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 LEU-ASP-PRO-GLU-THR-GLY-GLU-PHE-LEU


Mass: 1020.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16236*PLUS
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→65.32 Å / Num. obs: 11370 / % possible obs: 94.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.77
Reflection shellResolution: 2.6→2.81 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.451 / Num. unique obs: 2311 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→65.32 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.948 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.749 / ESU R Free: 0.351
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 786 6.9 %RANDOM
Rwork0.2017 ---
obs0.2069 10584 94.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.32 Å2 / Biso mean: 46.894 Å2 / Biso min: 26.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-1.08 Å20 Å2
2---2.17 Å20 Å2
3---3.25 Å2
Refinement stepCycle: final / Resolution: 2.6→65.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2257 0 4 73 2334
Biso mean--46.7 44.39 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192314
X-RAY DIFFRACTIONr_bond_other_d0.0020.021527
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9393150
X-RAY DIFFRACTIONr_angle_other_deg0.96133674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.715292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65522.636110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3915338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3121522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.45 59 -
Rwork0.331 700 -
obs--94.99 %

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