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- PDB-2vpj: Crystal structure of the Kelch domain of human KLHL12 -

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Basic information

Entry
Database: PDB / ID: 2vpj
TitleCrystal structure of the Kelch domain of human KLHL12
ComponentsKELCH-LIKE PROTEIN 12
KeywordsPROTEIN BINDING / ADAPTOR PROTEIN / WNT SIGNALING PATHWAY / PROTEIN-BINDING / UBIQUITIN DEGRADATION / UBL CONJUGATION PATHWAY / CUL3 / KELCH REPEAT / PHOSPHOPROTEIN / WNT SIGNALLING
Function / homology
Function and homology information


neural crest formation / neural crest cell development / COPII vesicle coating / COPII vesicle coat / COPII-coated ER to Golgi transport vesicle / Cul3-RING ubiquitin ligase complex / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / Degradation of DVL ...neural crest formation / neural crest cell development / COPII vesicle coating / COPII vesicle coat / COPII-coated ER to Golgi transport vesicle / Cul3-RING ubiquitin ligase complex / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / Degradation of DVL / centriolar satellite / Wnt signaling pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / intracellular membrane-bounded organelle / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Kelch-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / 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-type beta propeller / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / 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. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Kelch-like protein 12
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKeates, T. / Pike, A.C.W. / Bullock, A.N. / Salah, E. / Filippakopoulos, P. / Roos, A.K. / von Delft, F. / Savitsky, P. / Weigelt, J. / Edwards, A. ...Keates, T. / Pike, A.C.W. / Bullock, A.N. / Salah, E. / Filippakopoulos, P. / Roos, A.K. / von Delft, F. / Savitsky, P. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. / Knapp, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Cul3 Assembly with the Btb-Kelch Family of E3 Ubiquitin Ligases.
Authors: Canning, P. / Cooper, C.D.O. / Krojer, T. / Murray, J.W. / Pike, A.C.W. / Chaikuad, A. / Keates, T. / Thangaratnarajah, C. / Hojzan, V. / Marsden, B.D. / Gileadi, O. / Knapp, S. / von Delft, F. / Bullock, A.N.
History
DepositionFeb 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 6, 2013Group: Database references / Derived calculations / Structure summary
Revision 1.3Mar 27, 2013Group: Database references
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KELCH-LIKE PROTEIN 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0243
Polymers32,9061
Non-polymers1182
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.637, 61.546, 45.523
Angle α, β, γ (deg.)90.00, 111.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein KELCH-LIKE PROTEIN 12 / CUL3-INTERACTING PROTEIN 1


Mass: 32905.879 Da / Num. of mol.: 1 / Fragment: KELCH DOMAIN, RESIDUES 268-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q53G59
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 30.42 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE PH4.6, 30% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98068
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98068 Å / Relative weight: 1
ReflectionResolution: 1.85→42.3 Å / Num. obs: 19527 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 23.09 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DYH

2dyh


Resolution: 1.85→42.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.481 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 990 5.1 %RANDOM
Rwork0.161 ---
obs0.164 18504 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.31 Å2
2---1.58 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 8 132 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212245
X-RAY DIFFRACTIONr_bond_other_d0.0020.021444
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9483060
X-RAY DIFFRACTIONr_angle_other_deg0.98933512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53823.44193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5351514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
X-RAY DIFFRACTIONr_nbd_refined0.1890.2331
X-RAY DIFFRACTIONr_nbd_other0.2490.21563
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21071
X-RAY DIFFRACTIONr_nbtor_other0.1190.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2117
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.42931434
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.67452299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8688811
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.66811759
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 56
Rwork0.263 1282
Refinement TLS params.Method: refined / Origin x: 19.0429 Å / Origin y: 15.2531 Å / Origin z: 32.8648 Å
111213212223313233
T-0.0496 Å20.0023 Å2-0.0281 Å2--0.1046 Å20.0188 Å2---0.0782 Å2
L1.5672 °20.3244 °20.1457 °2-1.7945 °20.369 °2--0.8844 °2
S-0.0392 Å °-0.0182 Å °0.0063 Å °0.1644 Å °0.0205 Å °-0.1299 Å °0.0757 Å °0.0974 Å °0.0188 Å °

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