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- PDB-1x2j: Structural basis for the defects of human lung cancer somatic mut... -

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Basic information

Entry
Database: PDB / ID: 1x2j
TitleStructural basis for the defects of human lung cancer somatic mutations in the repression activity of Keap1 on Nrf2
ComponentsKelch-like ECH-associated protein 1
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


cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / centriolar satellite / inclusion body / cellular response to interleukin-4 / regulation of autophagy / actin filament / adherens junction / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / protein ubiquitination / negative regulation of gene expression / focal adhesion / regulation of DNA-templated transcription / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 ...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 / 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
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 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 25, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Kelch-like ECH-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4809
Polymers34,7121
Non-polymers7698
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.062, 103.062, 54.947
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: 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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 44048 / Num. obs: 41581 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.212 / % possible all: 68.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2 4149 random
Rwork0.168 --
obs0.173 41022 -
all-43976 -
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.06 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 40 346 2612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_improper_angle_d1.44
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011
RfactorNum. reflection% reflection
Rfree0.256 542 -
Rwork0.204 --
obs-5169 71.2 %

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