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- PDB-8uxs: KLHDC2 ubiquitin ligase in complex with a novel small-molecule -

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Basic information

Entry
Database: PDB / ID: 8uxs
TitleKLHDC2 ubiquitin ligase in complex with a novel small-molecule
ComponentsKelch domain-containing protein 2
KeywordsLIGASE / kelch repeat / beta-propeller / small-molecule / complex / substrate receptor / E3 / ubiquitin ligase
Function / homology
Function and homology information


ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / ubiquitin-like ligase-substrate adaptor activity / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear body / protein ubiquitination / nucleoplasm / nucleus
Similarity search - Function
: / Galactose oxidase, central domain / Kelch-type beta propeller
Similarity search - Domain/homology
: / Kelch domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRusnac, D.V. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: KLHDC2 ubiquitin ligase in complex with a novel small-molecule
Authors: Rusnac, D.V. / Zhou, G. / Canzani, D. / Bush, M.F. / DiMaio, F. / Zheng, N.
History
DepositionNov 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7484
Polymers77,9952
Non-polymers7532
Water4,702261
1
A: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3742
Polymers38,9981
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3742
Polymers38,9981
Non-polymers3761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.381, 88.165, 88.512
Angle α, β, γ (deg.)90.000, 104.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Kelch domain-containing protein 2


Mass: 38997.688 Da / Num. of mol.: 2 / Fragment: UNP residues 22-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y2U9
#2: Chemical ChemComp-XU8 / {4-[(2-{[(4-tert-butylphenyl)methyl]sulfanyl}acetamido)methyl]-1H-1,2,3-triazol-1-yl}acetic acid


Mass: 376.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.03 M MgCl2*6H2O, 0.03 M CaCl2*2H2O, 10% (w/v) PEG 20000, 20% (v/v) PEG MME, 0.1 M Tris (base)/ bicine pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→44.08 Å / Num. obs: 85458 / % possible obs: 70.05 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.45 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.076 / Net I/av σ(I): 7.2 / Net I/σ(I): 2967.5
Reflection shellResolution: 1.44→2.071 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.1776 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4409 / CC1/2: 0.597 / CC star: 0.865 / Rpim(I) all: 0.1132 / Rrim(I) all: 0.2113 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.08 Å / SU ML: 0.2035 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 19.5523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2018 2273 2.66 %
Rwork0.1661 83185 -
obs0.1671 85458 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.9 Å2
Refinement stepCycle: LAST / Resolution: 2→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 52 261 5497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235413
X-RAY DIFFRACTIONf_angle_d0.5757363
X-RAY DIFFRACTIONf_chiral_restr0.0442736
X-RAY DIFFRACTIONf_plane_restr0.0036947
X-RAY DIFFRACTIONf_dihedral_angle_d6.1796711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.26951500.22955178X-RAY DIFFRACTION96.75
2.04-2.090.24671330.20485190X-RAY DIFFRACTION97.19
2.09-2.140.24821380.19885149X-RAY DIFFRACTION97.13
2.14-2.20.21921440.18875273X-RAY DIFFRACTION97.89
2.2-2.270.19721430.19025140X-RAY DIFFRACTION96.83
2.27-2.340.24371500.17845210X-RAY DIFFRACTION97.15
2.34-2.420.23141420.17915155X-RAY DIFFRACTION97.69
2.42-2.520.22361380.17735099X-RAY DIFFRACTION95.32
2.52-2.630.18011390.17965124X-RAY DIFFRACTION95.12
2.63-2.770.23871380.17085230X-RAY DIFFRACTION97.32
2.77-2.950.21221420.185295X-RAY DIFFRACTION98.78
2.95-3.170.18891510.16215259X-RAY DIFFRACTION98.69
3.17-3.490.18891450.15655231X-RAY DIFFRACTION98.59
3.49-40.20321470.14195235X-RAY DIFFRACTION97.91
4-5.040.16061360.12465116X-RAY DIFFRACTION95.98
5.04-44.080.18591370.18215301X-RAY DIFFRACTION98.73

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