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- PDB-8in0: Structure of the Keap1 Kelch domain in complex with PGAM5-derived... -

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Basic information

Entry
Database: PDB / ID: 8in0
TitleStructure of the Keap1 Kelch domain in complex with PGAM5-derived peptide
Components
  • Kelch-like ECH-associated protein 1
  • PGAM5 12-mer peptide
KeywordsCYTOSOLIC PROTEIN / Kelch / PGAM5 derived peptide / Complex
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 / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity ...cellular response to carbohydrate stimulus / KEAP1-NFE2L2 pathway / regulation of epidermal cell differentiation / Neddylation / Antigen processing: Ubiquitination & Proteasome degradation / Ub-specific processing proteases / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / centriolar satellite / ubiquitin-like ligase-substrate adaptor activity / cellular response to interleukin-4 / inclusion body / 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-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 / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo (humans)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.8 Å
AuthorsJiang, L. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874343 China
CitationJournal: To Be Published
Title: Structure of the Keap1 Kelch domain in complex with PGAM5-derived peptide
Authors: Jiang, L. / Wang, C.
History
DepositionMar 8, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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: PGAM5 12-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0906
Polymers39,7062
Non-polymers3844
Water3,963220
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.655, 103.655, 56.167
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / INrf2


Mass: 38301.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Keap1, Inrf2, Kiaa0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X8
#2: Protein/peptide PGAM5 12-mer peptide


Mass: 1403.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo (humans)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, Lithium sulfate, Sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.8 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 1.8→24.704 Å / Num. obs: 31965 / % possible obs: 99.91 % / Redundancy: 5.8 % / CC1/2: 0.957 / Net I/σ(I): 14.68
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 3192 / CC1/2: 0.605

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.8→24.704 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.864 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.202 / SU B: 4.457 / SU ML: 0.124 / Average fsc free: 0.8143 / Average fsc work: 0.8256 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.154
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2847 1536 4.917 %
Rwork0.2533 29704 -
all0.255 --
obs-31240 97.485 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.466 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20.002 Å20 Å2
2--0.004 Å2-0 Å2
3----0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 20 220 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172081
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.6393230
X-RAY DIFFRACTIONr_angle_other_deg1.351.5724801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5065297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.32220.515136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24415355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6351523
X-RAY DIFFRACTIONr_chiral_restr0.0720.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02543
X-RAY DIFFRACTIONr_nbd_refined0.2090.2410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.22118
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2183
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.217
X-RAY DIFFRACTIONr_nbd_other0.1870.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.26
X-RAY DIFFRACTIONr_mcbond_it1.5941.6681194
X-RAY DIFFRACTIONr_mcbond_other1.5581.6671193
X-RAY DIFFRACTIONr_mcangle_it2.6132.4821489
X-RAY DIFFRACTIONr_mcangle_other2.6142.4841490
X-RAY DIFFRACTIONr_scbond_it2.1871.991180
X-RAY DIFFRACTIONr_scbond_other2.0991.9651162
X-RAY DIFFRACTIONr_scangle_it3.4052.8851741
X-RAY DIFFRACTIONr_scangle_other3.2882.8511717
X-RAY DIFFRACTIONr_lrange_it6.12720.1762655
X-RAY DIFFRACTIONr_lrange_other5.86219.8662601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3261340.2712226X-RAY DIFFRACTION99.873
1.847-1.8970.4841280.4311998X-RAY DIFFRACTION92.5958
1.897-1.9520.67990.671953X-RAY DIFFRACTION92.1419
1.952-2.0120.301890.2562074X-RAY DIFFRACTION99.6774
2.012-2.0780.288970.2252024X-RAY DIFFRACTION100
2.078-2.1510.2441000.2051913X-RAY DIFFRACTION100
2.151-2.2320.296650.2961715X-RAY DIFFRACTION90.8627
2.232-2.3230.529980.5291603X-RAY DIFFRACTION89.6679
2.323-2.4270.263830.21741X-RAY DIFFRACTION100
2.427-2.5450.219820.1791659X-RAY DIFFRACTION100
2.545-2.6830.278620.1871592X-RAY DIFFRACTION100
2.683-2.8450.256780.181482X-RAY DIFFRACTION100
2.845-3.0410.224970.1761374X-RAY DIFFRACTION100
3.041-3.2850.222580.1811319X-RAY DIFFRACTION100
3.285-3.5980.209760.1811178X-RAY DIFFRACTION98.6625
3.598-4.0220.23360.1881071X-RAY DIFFRACTION96.5126
4.022-4.6420.145570.124958X-RAY DIFFRACTION99.8033
4.642-5.6820.174430.151823X-RAY DIFFRACTION100
5.682-8.0190.175310.175652X-RAY DIFFRACTION100
8-100.152230.152349X-RAY DIFFRACTION95.6298

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