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- PDB-8cia: Crystal structure of the kelch domain of human KLHL20 -

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Basic information

Entry
Database: PDB / ID: 8cia
TitleCrystal structure of the kelch domain of human KLHL20
Components
  • (Kelch like family member 20) x 2
  • Kelch-like protein 20
KeywordsLIGASE / Kelch / E3 Ligase / KLHL20
Function / homology
Function and homology information


type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity / protein transport ...type II interferon binding / protein K33-linked ubiquitination / response to interferon-alpha / Golgi to endosome transport / Cul3-RING ubiquitin ligase complex / cytoskeleton organization / trans-Golgi network / PML body / ubiquitin-protein transferase activity / protein transport / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton / Neddylation / actin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / axon / dendrite / negative regulation of apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
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. ...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 family member 20 / Kelch like family member 20 / Kelch-like protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsSweeney, M.N. / Bradshaw, W.J. / Chen, Z. / Bullock, A.N.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Crystal structure of the kelch domain of human KLHL20
Authors: Sweeney, M.N. / Bradshaw, W.J. / Chen, Z. / Bullock, A.N.
History
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 20
B: Kelch like family member 20
C: Kelch-like protein 20
D: Kelch-like protein 20
E: Kelch like family member 20


Theoretical massNumber of molelcules
Total (without water)166,6085
Polymers166,6085
Non-polymers00
Water00
1
A: Kelch-like protein 20


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch like family member 20


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kelch-like protein 20


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kelch-like protein 20


Theoretical massNumber of molelcules
Total (without water)33,3211
Polymers33,3211
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kelch like family member 20


Theoretical massNumber of molelcules
Total (without water)33,3221
Polymers33,3221
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.928, 152.928, 195.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Kelch-like protein 20 / Kelch-like ECT2-interacting protein / Kelch-like protein X


Mass: 33321.414 Da / Num. of mol.: 3 / Mutation: C316A, C327A, C402A, C426A, C604A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL20, KLEIP, KLHLX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y2M5
#2: Protein Kelch like family member 20


Mass: 33321.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A673T7L2
#3: Protein Kelch like family member 20


Mass: 33322.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A452F0N4

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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: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG2000MME, 0.2M Trimethylamine N-Oxide, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.72→132.44 Å / Num. obs: 27259 / % possible obs: 95.8 % / Redundancy: 20.4 % / Biso Wilson estimate: 79.84 Å2 / CC1/2: 1 / Net I/σ(I): 8
Reflection shellResolution: 3.72→3.78 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1405 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.72→71.23 Å / SU ML: 0.4926 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2867 1356 4.98 %
Rwork0.2256 25873 -
obs0.2287 27229 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.57 Å2
Refinement stepCycle: LAST / Resolution: 3.72→71.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10843 0 0 0 10843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411068
X-RAY DIFFRACTIONf_angle_d0.7615027
X-RAY DIFFRACTIONf_chiral_restr0.0491631
X-RAY DIFFRACTIONf_plane_restr0.00721963
X-RAY DIFFRACTIONf_dihedral_angle_d5.70731604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.72-3.850.3641270.31362660X-RAY DIFFRACTION99.79
3.85-40.3002810.27491511X-RAY DIFFRACTION56.7
4-4.180.28871500.23682654X-RAY DIFFRACTION100
4.18-4.40.26131280.21362687X-RAY DIFFRACTION99.96
4.4-4.680.29761250.22512688X-RAY DIFFRACTION100
4.68-5.040.27471480.21392691X-RAY DIFFRACTION99.96
5.04-5.550.26291470.23142683X-RAY DIFFRACTION100
5.55-6.350.34161570.26192706X-RAY DIFFRACTION100
6.35-80.31361420.24282742X-RAY DIFFRACTION100
8-71.230.24021510.16582851X-RAY DIFFRACTION99.6

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