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- PDB-2lz1: Solution NMR Structure of the DNA-Binding Domain of Human NF-E2-R... -

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Basic information

Entry
Database: PDB / ID: 2lz1
TitleSolution NMR Structure of the DNA-Binding Domain of Human NF-E2-Related Factor 2, Northeast Structural Genomics Consortium (NESG) Target HR3520O
ComponentsNuclear factor erythroid 2-related factor 2
KeywordsTRANSCRIPTION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative
Function / homology
Function and homology information


aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / membraneless organelle / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response ...aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / membraneless organelle / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / positive regulation of ERAD pathway / PERK-mediated unfolded protein response / regulation of removal of superoxide radicals / negative regulation of vascular associated smooth muscle cell migration / regulation of cellular response to oxidative stress / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / positive regulation of ubiquitin-dependent protein catabolic process / mediator complex / 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 ferroptosis / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / negative regulation of cardiac muscle cell apoptotic process / 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 / 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 / cellular response to copper ion / cell redox homeostasis / protein-DNA complex / response to ischemia / transcription coregulator binding / positive regulation of D-glucose import / molecular condensate scaffold activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / response to oxidative stress / Potential therapeutics for SARS / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein ubiquitination / inflammatory response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / centrosome / ubiquitin protein ligase binding / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Transcription Factor Skn-1; Chain P / Transcription factor, Skn-1-like, DNA-binding domain / : / 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 ...Transcription Factor Skn-1; Chain P / Transcription factor, Skn-1-like, DNA-binding domain / : / 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 / Basic-leucine zipper domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Pulavarti, S.V.S.R.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of the DNA-Binding Domain of Human NF-E2-Related Factor 2, Northeast Structural Genomics Consortium (NESG) Target HR3520O
Authors: Eletsky, A. / Pulavarti, S.V.S.R.K. / Lee, D. / Kohan, E. / Janjua, H. / Xiao, R. / Acton, T.B. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionSep 22, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear factor erythroid 2-related factor 2


Theoretical massNumber of molelcules
Total (without water)10,6671
Polymers10,6671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 10667.446 Da / Num. of mol.: 1 / Fragment: DNA-binding domain residues 445-523
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFE2L2, NRF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q16236

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1612D 1H-13C HSQC aromatic
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HBHA(CO)NH
1913D HN(CA)CO
11013D (H)CCH-TOCSY aliphatic
11113D (H)CCH-COSY aliphatic
11222D 1H-13C HSQC methyl
11311D 15N T1
11411D 15N T2

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] HR3520O, 50 uM DSS, 0.02 % sodium azide, 50 mM Arginine, 10 mM DTT, 50 mM ammonium acetate, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [5% 13C; U-100% 15N] HR3520O, 50 uM DSS, 0.02 % sodium azide, 50 mM Arginine, 10 mM DTT, 50 mM ammonium acetate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMHR3520O-1[U-100% 13C; U-100% 15N]1
50 uMDSS-21
0.02 %sodium azide-31
50 mMArginine-41
10 mMDTT-51
50 mMammonium acetate-61
0.5 mMHR3520O-7[5% 13C; U-100% 15N]2
50 uMDSS-82
0.02 %sodium azide-92
50 mMArginine-102
10 mMDTT-112
50 mMammonium acetate-122
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AS-DP1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
VnmrJ2.2DVariancollection
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PSVS1.4Bhattacharya, Montelionestructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS ...Details: STRUCTURE DETERMINATION WAS PERFORMED BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN ITERATIVE REFINEMENT WITH CYANA. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE FIELD
NMR constraintsNOE constraints total: 802 / NOE intraresidue total count: 291 / NOE long range total count: 101 / NOE medium range total count: 188 / NOE sequential total count: 222 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 42 / Protein psi angle constraints total count: 42
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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