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- PDB-4hxi: Crystal structure of KLHL3/Cul3 complex -

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Basic information

Entry
Database: PDB / ID: 4hxi
TitleCrystal structure of KLHL3/Cul3 complex
Components
  • Cullin-3
  • Kelch-like protein 3
KeywordsPROTEIN BINDING / BTB-BACK / Protein-protein interaction
Function / homology
Function and homology information


distal tubule morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / monoatomic ion homeostasis / POZ domain binding / renal sodium ion absorption / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating ...distal tubule morphogenesis / positive regulation of mitotic cell cycle phase transition / trophectodermal cellular morphogenesis / liver morphogenesis / monoatomic ion homeostasis / POZ domain binding / renal sodium ion absorption / nuclear protein quality control by the ubiquitin-proteasome system / polar microtubule / COPII vesicle coating / anaphase-promoting complex-dependent catabolic process / regulation protein catabolic process at postsynapse / RHOBTB3 ATPase cycle / cell projection organization / positive regulation of mitotic metaphase/anaphase transition / embryonic cleavage / potassium ion homeostasis / stem cell division / Notch binding / fibroblast apoptotic process / RHOBTB1 GTPase cycle / negative regulation of type I interferon production / Cul3-RING ubiquitin ligase complex / mitotic metaphase chromosome alignment / ubiquitin ligase complex scaffold activity / negative regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of cytokinesis / cullin family protein binding / sperm flagellum / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / RHOBTB2 GTPase cycle / protein autoubiquitination / gastrulation / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / intrinsic apoptotic signaling pathway / cyclin binding / positive regulation of protein ubiquitination / kidney development / integrin-mediated signaling pathway / cellular response to amino acid stimulus / Degradation of DVL / macroautophagy / Hedgehog 'on' state / protein destabilization / Wnt signaling pathway / G1/S transition of mitotic cell cycle / Regulation of RAS by GAPs / protein polyubiquitination / spindle pole / mitotic spindle / KEAP1-NFE2L2 pathway / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell migration / Neddylation / actin binding / cellular response to oxidative stress / ubiquitin-dependent protein catabolic process / gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / cytoskeleton / postsynapse / protein ubiquitination / inflammatory response / positive regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / structural molecule activity / negative regulation of transcription by RNA polymerase II / Golgi apparatus / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kelch-like protein 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Kelch ...Kelch-like protein 3 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #420 / Cullin Repeats / 5 helical Cullin repeat like / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Cullin protein neddylation domain / Kelch / Kelch motif / Kelch repeat type 1 / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cullin-3 / Kelch-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.513 Å
AuthorsJi, A.X. / Prive, G.G.
CitationJournal: Plos One / Year: 2013
Title: Crystal structure of KLHL3 in complex with Cullin3.
Authors: Ji, A.X. / Prive, G.G.
History
DepositionNov 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like protein 3
B: Cullin-3


Theoretical massNumber of molelcules
Total (without water)76,5762
Polymers76,5762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.770, 228.677, 239.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Kelch-like protein 3


Mass: 31366.789 Da / Num. of mol.: 1 / Fragment: BTB-BACK / Mutation: K87A, K89A, K90A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL3, KIAA1129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UH77
#2: Protein Cullin-3 / CUL-3


Mass: 45209.664 Da / Num. of mol.: 1 / Fragment: NTD / Mutation: K274R, I342R, L346D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL3, KIAA0617 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13618

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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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M ammonium tartrate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2012
RadiationMonochromator: Double Si 111, Double Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→20 Å / Num. obs: 49265 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.5→3.56 Å / % possible all: 95.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.513→20 Å / SU ML: 0.42 / σ(F): 0 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 1316 10.08 %Random
Rwork0.2441 ---
all0.2476 ---
obs0.2476 13785 89.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.513→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 0 0 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044404
X-RAY DIFFRACTIONf_angle_d0.8635932
X-RAY DIFFRACTIONf_dihedral_angle_d14.4491663
X-RAY DIFFRACTIONf_chiral_restr0.068669
X-RAY DIFFRACTIONf_plane_restr0.003769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5126-3.65240.30981280.29051183X-RAY DIFFRACTION82
3.6524-3.81760.31931420.26271256X-RAY DIFFRACTION89
3.8176-4.01730.2831450.24371256X-RAY DIFFRACTION87
4.0173-4.26680.26861450.23811274X-RAY DIFFRACTION90
4.2668-4.59260.25281510.20931333X-RAY DIFFRACTION92
4.5926-5.04810.28311480.20561333X-RAY DIFFRACTION91
5.0481-5.76340.2911470.25051338X-RAY DIFFRACTION92
5.7634-7.20530.30631520.29561350X-RAY DIFFRACTION91
7.2053-20.09740.2531580.24021413X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -5.5498 Å / Origin y: -27.3909 Å / Origin z: -7.2261 Å
111213212223313233
T0.0105 Å20.0034 Å2-0.2275 Å2-0.2957 Å20.0262 Å2---0.2244 Å2
L1.2564 °20.6395 °2-0.9331 °2-1.9712 °2-0.5413 °2--1.0218 °2
S-0.1703 Å °0.3438 Å °-0.1472 Å °-0.3133 Å °0.1305 Å °-0.2499 Å °-0.082 Å °-0.4893 Å °-0.1463 Å °
Refinement TLS groupSelection details: all

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