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- PDB-8pif: Fragment 12 in complex with KLHDC2 -

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Basic information

Entry
Database: PDB / ID: 8pif
TitleFragment 12 in complex with KLHDC2
ComponentsKelch domain-containing protein 2
KeywordsLIGASE / Cul2-RING ubiquitin ligase complex
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
2-(furan-3-yl)ethanoic acid / Kelch domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsBoettcher, J. / Mayer, M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: KLHDC2 - The Next Level
Authors: Boettcher, J.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 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

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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)83,0175
Polymers82,7022
Non-polymers3143
Water9,548530
1
A: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5393
Polymers41,3511
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kelch domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4772
Polymers41,3511
Non-polymers1261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.261, 88.308, 88.922
Angle α, β, γ (deg.)90, 104.51, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1


Mass: 41351.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2U9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-YW6 / 2-(furan-3-yl)ethanoic acid


Mass: 126.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 23%PEG3350 100mM HEPES pH 7.0 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000018 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000018 Å / Relative weight: 1
ReflectionResolution: 1.782→61.6419 Å / Num. obs: 43588 / % possible obs: 69 % / Redundancy: 7 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 11.3
Reflection shellResolution: 1.782→1.958 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.262 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2179 / Rsym value: 1.262 / % possible all: 14.1

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XDSFeb 5, 2021data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.782→35.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.688 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.199 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 2155 -RANDOM
Rwork0.1817 ---
obs0.1833 43579 69 %-
Displacement parametersBiso mean: 32.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.4428 Å20 Å2-0.5369 Å2
2--1.4934 Å20 Å2
3---0.9493 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.782→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 22 530 5662
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00910136HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9818150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2845SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1659HARMONIC5
X-RAY DIFFRACTIONt_it5303HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion638SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8579SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.4
X-RAY DIFFRACTIONt_other_torsion15.27
LS refinement shellResolution: 1.782→1.89 Å
RfactorNum. reflection% reflection
Rfree0.2496 39 -
Rwork0.255 --
obs--8.55 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.31250.0471-0.13440.75-0.01241.5273-0.0577-0.0157-0.0638-0.01570.06630.0339-0.06380.0339-0.0085-0.0639-0.0542-0.0132-0.0242-0.0023-0.02669.1483-0.030621.804
21.76840.10990.12920.7237-0.19241.3213-0.0491-0.01920.0621-0.01920.0413-0.01940.0621-0.01940.0078-0.0681-0.05220.0007-0.03840.019-0.0229-9.248942.837622.9353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A28 - 359
2X-RAY DIFFRACTION1{ A|* }A401
3X-RAY DIFFRACTION2{ B|* }B27 - 359

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