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- PDB-1x2r: Structural basis for the defects of human lung cancer somatic mut... -

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Basic information

Entry
Database: PDB / ID: 1x2r
TitleStructural basis for the defects of human lung cancer somatic mutations in the repression activity of Keap1 on Nrf2
Components
  • Kelch-like ECH-associated protein 1
  • Nuclear factor erythroid 2 related factor 2
KeywordsTRANSCRIPTION / beta propeller / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of glutathione biosynthetic process / aflatoxin catabolic 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 / cellular response to carbohydrate stimulus / regulation of cellular response to oxidative stress / regulation of removal of superoxide radicals ...positive regulation of glutathione biosynthetic process / aflatoxin catabolic 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 / cellular response to carbohydrate stimulus / regulation of cellular response to oxidative stress / regulation of removal of superoxide radicals / KEAP1-NFE2L2 pathway / negative regulation of vascular associated smooth muscle cell migration / regulation of epidermal cell differentiation / Neddylation / cellular response to laminar fluid shear stress / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / cellular response to fluid shear stress / cellular response to angiotensin / negative regulation of cardiac muscle cell apoptotic process / proteasomal ubiquitin-independent protein catabolic process / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / regulation of embryonic development / transcription factor binding / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / positive regulation of blood vessel endothelial cell migration / cellular response to interleukin-4 / 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 / inclusion body / endoplasmic reticulum unfolded protein response / cellular response to copper ion / response to endoplasmic reticulum stress / cell redox homeostasis / response to organic substance / regulation of autophagy / response to ischemia / transcription coregulator binding / actin filament / protein-DNA complex / positive regulation of glucose import / adherens junction / cellular response to hydrogen peroxide / positive regulation of neuron projection development / 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 oxidative stress / cellular response to tumor necrosis factor / midbody / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / in utero embryonic development / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / protein ubiquitination / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / focal adhesion / centrosome / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / 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-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 repeat type 1 / Kelch motif / 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 / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / 6 Propeller / Neuraminidase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPadmanabhan, B. / Tong, K.I. / Nakamura, Y. / Ohta, T. / Scharlock, M. / Kobayashi, A. / Ohtsuji, M. / Kang, M.-I. / Yamamoto, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Mol.Cell / Year: 2006
Title: Structural basis for defects of keap1 activity provoked by its point mutations in lung cancer
Authors: Padmanabhan, B. / Tong, K.I. / Ohta, T. / Nakamura, Y. / Scharlock, M. / Ohtsuji, M. / Kang, M.-I. / Kobayashi, A. / Yokoyama, S. / Yamamoto, M.
History
DepositionApr 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Nuclear factor erythroid 2 related factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,62911
Polymers35,7642
Non-polymers8659
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-111 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.349, 103.349, 55.235
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 / Cytosolic inhibitor of Nrf2


Mass: 34711.906 Da / Num. of mol.: 1 / Fragment: keap1-dc, residues 309-624
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 Nuclear factor erythroid 2 related factor 2 / NF-E2 related factor 2 / NFE2-related factor 2 / Nuclear factor / erythroid derived 2 / like 2


Mass: 1052.089 Da / Num. of mol.: 1 / Fragment: Nrf2/Neh2 peptide, residues 76-84 / Source method: obtained synthetically / Details: Nrf2 peptide, synthetic peptide / References: UniProt: Q60795
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.4 Å3/Da / Density % sol: 49 %
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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2005 / Details: mirrors
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 37155 / Num. obs: 35557 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3 % / Rmerge(I) obs: 0.167 / % possible all: 77.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Keap1-DC native structure - 1X2J

1x2j


Resolution: 1.7→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.214 1739 random
Rwork0.191 --
obs0.196 35531 -
all-37127 -
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 45 424 2769
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.26 249 -
Rwork0.227 --
obs-5008 81.8 %

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