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- PDB-2dyh: Crystal structure of the Keap1 protein in complexed with the N-te... -

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Basic information

Entry
Database: PDB / ID: 2dyh
TitleCrystal structure of the Keap1 protein in complexed with the N-terminal region of the Nrf2 transcription factor
Components
  • Kelch-like ECH-associated protein 1
  • Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2
KeywordsTRANSCRIPTION / bet-propeller / Kelch motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 methionine / cellular response to fluid shear stress / 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 factor binding / 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 / response to endoplasmic reticulum stress / cell redox homeostasis / transcription coregulator binding / response to ischemia / positive regulation of D-glucose import / actin filament / 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 / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription cis-regulatory region binding / regulation of autophagy / 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 DNA-templated transcription / 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 / 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-type beta propeller / Kelch-like ECH-associated protein 1 / : / 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-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 / 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. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
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: 1.9 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Different electrostatic potentials define ETGE and DLG motifs as hinge and latch in oxidative stress response
Authors: Tong, K.I. / Padmanabhan, B. / Kobayashi, A. / Shang, C. / Hirotsu, Y. / Yokoyama, S. / Yamamoto, M.
History
DepositionSep 14, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
B: Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4809
Polymers36,8072
Non-polymers6727
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.131, 103.131, 56.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Kelch-like ECH-associated protein 1 / Keap1 / Cytosolic inhibitor of Nrf2


Mass: 35006.277 Da / Num. of mol.: 1 / Fragment: Keap1-DC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)_RIL / References: UniProt: Q9Z2X8
#2: Protein/peptide Nrf2/Neh2 peptide from Nuclear factor erythroid 2-related factor 2 / NF-E2-related factor 2 / NFE2-related factor 2 / Nuclear factor / erythroid derived 2 / like 2


Mass: 1801.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Nrf2 peptide, synthetic peptide / References: UniProt: Q60795
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium sulfate, Lithium Sulfate, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 27043 / Num. obs: 26542 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.398 / Num. unique all: 2359 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DNAdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X2J

1x2j


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.172 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21102 1335 5 %RANDOM
Rwork0.17237 ---
obs0.17432 25143 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 35 307 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212405
X-RAY DIFFRACTIONr_angle_refined_deg1.551.953275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52422.895114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8111522
X-RAY DIFFRACTIONr_chiral_restr0.1180.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021874
X-RAY DIFFRACTIONr_nbd_refined0.2210.21078
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.227
X-RAY DIFFRACTIONr_mcbond_it1.1421.51532
X-RAY DIFFRACTIONr_mcangle_it1.80822388
X-RAY DIFFRACTIONr_scbond_it2.69131014
X-RAY DIFFRACTIONr_scangle_it3.814.5887
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 92 -
Rwork0.219 1621 -
obs--86.43 %

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