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- PDB-7o7b: Solution NMR Structure of the Neh1 Domain of Human Nuclear factor... -

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Basic information

Entry
Database: PDB / ID: 7o7b
TitleSolution NMR Structure of the Neh1 Domain of Human Nuclear factor erythroid 2-related factor 2 (NRF2)
ComponentsIsoform 3 of Nuclear factor erythroid 2-related factor 2
KeywordsDNA BINDING PROTEIN / cap n collar (CNC) / basic leucine zipper (bZIP) transcription factor / antioxidant response
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of cellular response to oxidative stress ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic process / negative regulation of hematopoietic stem cell differentiation / Regulation of HMOX1 expression and activity / integrated stress response signaling / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of cellular response to oxidative stress / negative regulation of vascular associated smooth muscle cell migration / regulation of removal of superoxide radicals / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / positive regulation of ubiquitin-dependent protein catabolic process / NFE2L2 regulating inflammation associated genes / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / cellular response to angiotensin / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of cardiac muscle cell apoptotic process / NFE2L2 regulating anti-oxidant/detoxification enzymes / NFE2L2 regulating tumorigenic genes / proteasomal ubiquitin-independent protein catabolic process / regulation of innate immune response / regulation of embryonic development / positive regulation of blood vessel endothelial cell migration / positive regulation of blood coagulation / cellular response to glucose starvation / negative regulation of endothelial cell apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / cellular response to copper ion / cell redox homeostasis / response to ischemia / transcription coregulator binding / positive regulation of glucose import / protein-DNA complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / 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 / KEAP1-NFE2L2 pathway / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Neddylation / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / centrosome / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / 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 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain
Similarity search - Domain/homology
Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBrueschweiler, S.
Funding support Austria, 1items
OrganizationGrant numberCountry
Christian Doppler Forschungsgesellschaft Austria
CitationJournal: Chemmedchem / Year: 2021
Title: A Step toward NRF2-DNA Interaction Inhibitors by Fragment-Based NMR Methods.
Authors: Bruschweiler, S. / Fuchs, J.E. / Bader, G. / McConnell, D.B. / Konrat, R. / Mayer, M.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 3 of Nuclear factor erythroid 2-related factor 2


Theoretical massNumber of molelcules
Total (without water)9,4221
Polymers9,4221
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6940 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Isoform 3 of Nuclear factor erythroid 2-related factor 2 / NF-E2-related factor 2 / NFE2-related factor 2 / Nrf-2 / HEBP1 / Nuclear factor / erythroid derived 2 / like 2


Mass: 9422.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFE2L2, NRF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16236

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D HN(CO)CA
131isotropic23D HNCO
141isotropic23D HN(CA)CO
151isotropic23D CBCA(CO)NH
161isotropic23D HN(CA)CB
171isotropic23D (H)CCONNH
181isotropic13D (H)CCH-TOCSY
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-15N NOESY
1111isotropic12D 1H-13C HSQC
1121isotropic12D 1H-15N HSQC

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-100% 13C; U-100% 15N] neh1, 95% H2O/5% D2O
Label: Neh1 / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.5 mM / Component: neh1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 150 mM / Label: neh1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD8001
Bruker Avance NOEBrukerAvance NOE6002

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Processing

NMR software
NameDeveloperClassification
CCNMRSkinner, Fogh, Boucher, Ragan, Mureddu, and Vuisterdata analysis
ARIALinge, O'Donoghue and Nilgesstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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