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- PDB-7yen: Crystal structure of the Keap1 Kelch domain in complex with Caffe... -

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Basic information

Entry
Database: PDB / ID: 7yen
TitleCrystal structure of the Keap1 Kelch domain in complex with Caffeic acid
ComponentsKelch-like ECH-associated protein 1
KeywordsCYTOSOLIC PROTEIN / Kelch -like ECH-associated protein 1
Function / homology
Function and homology information


regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body ...regulation of epidermal cell differentiation / Neddylation / Ub-specific processing proteases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / transcription regulator inhibitor activity / inclusion body / cellular response to interleukin-4 / actin filament / centriolar satellite / disordered domain specific binding / cellular response to oxidative stress / midbody / ubiquitin-dependent protein catabolic process / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA polymerase II-specific DNA-binding transcription factor binding / regulation of autophagy / protein ubiquitination / regulation of DNA-templated transcription / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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 motif / Kelch / Kelch repeat type 1 / 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 motif / Kelch / Kelch repeat type 1 / 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
CAFFEIC ACID / Kelch-like ECH-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 2.8 Å
AuthorsWang, C. / Jiang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81930114 China
CitationJournal: To Be Published
Title: Structure of the Keap1 Kelch domain complexed with Caffeic acid
Authors: Wang, C. / Jiang, L.
History
DepositionJul 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,38212
Polymers32,2711
Non-polymers1,11111
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.080, 103.080, 54.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Kelch-like ECH-associated protein 1 / Cytosolic inhibitor of Nrf2 / INrf2


Mass: 32271.133 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

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Non-polymers , 5 types, 23 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Ammonium sulfate, Lithium sulfate, Sodium citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 2 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.8→23.328 Å / Num. obs: 8306 / % possible obs: 99.772 % / Redundancy: 7.8 % / CC1/2: 0.998 / Net I/σ(I): 45.15
Reflection shellResolution: 2.8→2.871 Å / Num. unique obs: 8308 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.8→23.328 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.881 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.18 / SU B: 13.516 / SU ML: 0.256 / Average fsc free: 0.9071 / Average fsc work: 0.9318 / Cross valid method: FREE R-VALUE / ESU R Free: 0.363
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2369 366 4.408 %
Rwork0.1827 7937 -
all0.185 --
obs-8303 99.772 %
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: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.226 Å2-0.613 Å2-0 Å2
2---1.226 Å20 Å2
3---3.978 Å2
Refinement stepCycle: LAST / Resolution: 2.8→23.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2226 0 62 12 2300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132333
X-RAY DIFFRACTIONr_bond_other_d0.0050.0172012
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.6373179
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5714642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7715289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.64920.538130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28915337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5651521
X-RAY DIFFRACTIONr_chiral_restr0.0640.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
X-RAY DIFFRACTIONr_nbd_refined0.2010.2429
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.22023
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21051
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0730.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.216
X-RAY DIFFRACTIONr_nbd_other0.2370.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0990.27
X-RAY DIFFRACTIONr_mcbond_it0.8981.0141160
X-RAY DIFFRACTIONr_mcbond_other0.8951.011158
X-RAY DIFFRACTIONr_mcangle_it1.6451.5121447
X-RAY DIFFRACTIONr_mcangle_other1.6451.5151448
X-RAY DIFFRACTIONr_scbond_it1.1841.2661173
X-RAY DIFFRACTIONr_scbond_other1.1841.2691174
X-RAY DIFFRACTIONr_scangle_it1.9371.8471732
X-RAY DIFFRACTIONr_scangle_other1.9361.851733
X-RAY DIFFRACTIONr_lrange_it4.62611.9922461
X-RAY DIFFRACTIONr_lrange_other4.62512.0012462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.342350.273579X-RAY DIFFRACTION100
2.873-2.9510.41250.252560X-RAY DIFFRACTION100
2.951-3.0370.409140.239567X-RAY DIFFRACTION100
3.037-3.130.284190.223548X-RAY DIFFRACTION100
3.13-3.2330.303130.206539X-RAY DIFFRACTION100
3.233-3.3460.342190.189491X-RAY DIFFRACTION100
3.346-3.4720.225240.193483X-RAY DIFFRACTION100
3.472-3.6140.183270.173472X-RAY DIFFRACTION100
3.614-3.7740.249250.157431X-RAY DIFFRACTION100
3.774-3.9580.201230.157445X-RAY DIFFRACTION100
3.958-4.1720.15200.135407X-RAY DIFFRACTION99.7664
4.172-4.4240.149250.125374X-RAY DIFFRACTION100
4.424-4.7290.10560.13381X-RAY DIFFRACTION100
4.729-5.1070.184160.123339X-RAY DIFFRACTION100
5.107-5.5920.198150.172312X-RAY DIFFRACTION100
5.592-6.2490.234150.184290X-RAY DIFFRACTION100
6.249-7.210.222100.208256X-RAY DIFFRACTION100
7.21-8.8160.215210.2211X-RAY DIFFRACTION100
8.816-12.4070.24100.159165X-RAY DIFFRACTION100
12.407-23.3280.43840.26787X-RAY DIFFRACTION84.2593

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