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- PDB-4ifl: Crystal Structures of apo Keap1, Keap1-peptide, and Keap1-compoun... -

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Basic information

Entry
Database: PDB / ID: 4ifl
TitleCrystal Structures of apo Keap1, Keap1-peptide, and Keap1-compound complexes
Components
  • Nrf2 peptide
  • kelch-like ECH-associated protein 1
KeywordsTRANSCRIPTION / PROTEIN BINDING
Function / homology
Function and homology information


aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of removal of superoxide radicals ...aflatoxin catabolic process / positive regulation of glutathione biosynthetic process / negative regulation of hematopoietic stem cell differentiation / integrated stress response signaling / Regulation of HMOX1 expression and activity / negative regulation of cellular response to hypoxia / NFE2L2 regulating TCA cycle genes / PERK-mediated unfolded protein response / positive regulation of ERAD pathway / regulation of removal of superoxide radicals / regulation of cellular response to oxidative stress / regulation of epidermal cell differentiation / cellular response to laminar fluid shear stress / NFE2L2 regulating ER-stress associated genes / NFE2L2 regulating inflammation associated genes / mediator complex / cellular response to methionine / cellular response to fluid shear stress / NFE2L2 regulates pentose phosphate pathway genes / NFE2L2 regulating MDR associated enzymes / positive regulation of ubiquitin-dependent protein catabolic process / Nuclear events mediated by NFE2L2 / Regulation of NFE2L2 gene expression / negative regulation of response to oxidative stress / negative regulation of ferroptosis / negative regulation of cardiac muscle cell apoptotic process / NFE2L2 regulating tumorigenic genes / NFE2L2 regulating anti-oxidant/detoxification enzymes / proteasomal ubiquitin-independent protein catabolic process / Cul3-RING ubiquitin ligase complex / regulation of innate immune response / 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 / cell redox homeostasis / transcription coregulator binding / response to ischemia / positive regulation of D-glucose import / actin filament / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Heme signaling / 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 / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to xenobiotic stimulus / cellular response to tumor necrosis factor / Neddylation / DNA-binding transcription activator activity, RNA polymerase II-specific / midbody / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / regulation of autophagy / Ub-specific processing proteases / 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 transcription by RNA polymerase II / 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 / DNA binding
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 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated ...: / 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 / : / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / 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
Kelch-like ECH-associated protein 1 / Nuclear factor erythroid 2-related factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. ...Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. / Yao, N. / Artis, D.R.
CitationJournal: Acta Crystallogr.,Sect.D
Title: Crystal Structures of apo Keap1, Keap1-peptide, and Keap1-compound complexes
Authors: Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. ...Authors: Pan, H. / Lin, M. / Yang, Y. / Callaway, K. / Baker, J. / Diep, L. / Yan, J. / Tanaka, K. / Zhu, Y.L. / Konradi, A.W. / Jobling, M. / Tam, D. / Ren, Z. / Cheung, H. / Bova, M. / Riley, B.E. / Yao, N. / Artis, D.R.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: kelch-like ECH-associated protein 1
P: Nrf2 peptide


Theoretical massNumber of molelcules
Total (without water)33,6872
Polymers33,6872
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint1 kcal/mol
Surface area13030 Å2
MethodPISA
2
X: kelch-like ECH-associated protein 1
P: Nrf2 peptide

X: kelch-like ECH-associated protein 1
P: Nrf2 peptide


Theoretical massNumber of molelcules
Total (without water)67,3734
Polymers67,3734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4070 Å2
ΔGint-8 kcal/mol
Surface area24040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.499, 92.030, 46.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein kelch-like ECH-associated protein 1


Mass: 31828.525 Da / Num. of mol.: 1 / Fragment: Kelch domain, UNP residues 321-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KEAP1, INRF2, KIAA0132, KLHL19 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14145
#2: Protein/peptide Nrf2 peptide


Mass: 1858.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16236*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium Fluoride, 0.1 M Bis-Tris Propance pH 7.5, 20 % PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 20, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→39.66 Å / Num. all: 29768 / Num. obs: 26303 / % possible obs: 88.36 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.847 Å / % possible all: 44.54

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
REFMAC5.5.0102refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.116 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 1394 5 %RANDOM
Rwork0.19048 ---
all0.1927 29768 --
obs0.19274 26303 88.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2322 0 0 301 2623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0212378
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9373235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6815299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72122.845116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99215350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7681522
X-RAY DIFFRACTIONr_chiral_restr0.1760.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211881
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3321.51481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10722368
X-RAY DIFFRACTIONr_scbond_it3.6013897
X-RAY DIFFRACTIONr_scangle_it5.5474.5867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.606 40 -
Rwork0.431 980 -
obs--44.54 %

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