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- PDB-8rbh: Crystal structure of the kelch domain of human KLHL12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 8rbh
TitleCrystal structure of the kelch domain of human KLHL12 in complex with PEF1 peptide
Components
  • Kelch-like protein 12
  • Peflin
KeywordsLIGASE / E3 ligase / protein binding / peptide binding / Kelch-like protein / kelch like family member 12.
Function / homology
Function and homology information


neural crest formation / neural crest cell development / COPII vesicle coating / COPII vesicle coat / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / COPII-coated ER to Golgi transport vesicle / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity ...neural crest formation / neural crest cell development / COPII vesicle coating / COPII vesicle coat / positive regulation of protein monoubiquitination / Cul3-RING ubiquitin ligase complex / COPII-coated ER to Golgi transport vesicle / protein monoubiquitination / endoplasmic reticulum to Golgi vesicle-mediated transport / ubiquitin-like ligase-substrate adaptor activity / Degradation of DVL / centriolar satellite / Wnt signaling pathway / response to calcium ion / calcium-dependent protein binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein dimerization activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum / RNA binding / extracellular exosome / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / EF-hand domain / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 ...: / EF-hand domain / KLHDC2/KLHL20/DRC7 Kelch-repeats domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch motif / Kelch repeat type 1 / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Kelch-like protein 12 / Peflin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRamdass, A.E. / Chen, Z. / Dalietou, E.V. / Manning, C.E. / Bullock, A.N.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510
CitationJournal: To Be Published
Title: Structural basis for co-adaptor and antagonist binding to the KLHL12 E3 ligase
Authors: Ramdass, A.E. / Dalietou, E.V. / Chen, Z. / Platt, M. / Aitmakhanova, K. / Fedorov, O. / Bullock, A.N.
History
DepositionDec 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kelch-like protein 12
B: Kelch-like protein 12
C: Peflin
D: Peflin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9689
Polymers67,8144
Non-polymers1545
Water6,269348
1
A: Kelch-like protein 12
C: Peflin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9924
Polymers33,9072
Non-polymers852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area11710 Å2
MethodPISA
2
B: Kelch-like protein 12
D: Peflin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9765
Polymers33,9072
Non-polymers693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-44 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.001, 78.390, 73.784
Angle α, β, γ (deg.)90.000, 99.240, 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-like protein 12 / CUL3-interacting protein 1 / DKIR homolog / hDKIR


Mass: 32905.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL12, C3IP1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53G59
#2: Protein/peptide Peflin / PEF protein with a long N-terminal hydrophobic domain / Penta-EF hand domain-containing protein 1


Mass: 1001.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UBV8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 1.99 Å3/Da / Density % sol: 38.31 % / Description: Needle
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M BIS-TRIS pH 5.5, 200 mM NaCl, and 30% PEG4K. (1:1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.88→72.83 Å / Num. obs: 40172 / % possible obs: 97.58 % / Redundancy: 6.928 % / Biso Wilson estimate: 26.91 Å2 / CC1/2: 0.9915 / Rmerge(I) obs: 0.2826 / Rpim(I) all: 0.115 / Rrim(I) all: 0.306 / Net I/σ(I): 6.2
Reflection shellResolution: 1.88→1.91 Å / Rmerge(I) obs: 3.843 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1936 / CC1/2: 0.189 / Rpim(I) all: 1.562 / Rrim(I) all: 4.154 / % possible all: 94.58

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→72.83 Å / SU ML: 0.2955 / Cross valid method: FREE R-VALUE / Phase error: 29.846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2576 1986 4.96 %
Rwork0.2096 38029 -
obs0.212 40015 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.14 Å2
Refinement stepCycle: LAST / Resolution: 1.88→72.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4418 0 8 348 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084549
X-RAY DIFFRACTIONf_angle_d1.00996213
X-RAY DIFFRACTIONf_chiral_restr0.0625698
X-RAY DIFFRACTIONf_plane_restr0.0083806
X-RAY DIFFRACTIONf_dihedral_angle_d14.81361584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.37921190.35292630X-RAY DIFFRACTION93.85
1.93-1.980.35221400.32682633X-RAY DIFFRACTION95.85
1.98-2.040.35291580.30732687X-RAY DIFFRACTION96.15
2.04-2.10.31311380.28032674X-RAY DIFFRACTION96.24
2.1-2.180.3081420.26672669X-RAY DIFFRACTION96.66
2.18-2.270.31741460.25592700X-RAY DIFFRACTION96.87
2.27-2.370.30921480.24082737X-RAY DIFFRACTION97.37
2.37-2.490.31761410.24112715X-RAY DIFFRACTION97.47
2.49-2.650.31591370.22772733X-RAY DIFFRACTION97.89
2.65-2.860.27831500.21632685X-RAY DIFFRACTION97.59
2.86-3.140.27281510.19312762X-RAY DIFFRACTION98.41
3.14-3.60.2421260.17792782X-RAY DIFFRACTION98.64
3.6-4.530.18961320.14862799X-RAY DIFFRACTION98.95
4.53-72.830.19561580.19012823X-RAY DIFFRACTION98.87

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