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

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Basic information

Entry
Database: PDB / ID: 8oio
TitleCrystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide
Components
  • Kelch-like protein 12
  • Pleckstrin homology domain-containing family A member 4
KeywordsLIGASE / Inhibitor / Complex / Interaction Motif / KLHL12 / PLEKHA4
Function / homology
Function and homology information


neural crest formation / neural crest cell development / COPII vesicle coat / COPII vesicle coating / positive regulation of Wnt signaling pathway, planar cell polarity pathway / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Cul3-RING ubiquitin ligase complex / COPII-coated ER to Golgi transport vesicle ...neural crest formation / neural crest cell development / COPII vesicle coat / COPII vesicle coating / positive regulation of Wnt signaling pathway, planar cell polarity pathway / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / Cul3-RING ubiquitin ligase complex / COPII-coated ER to Golgi transport vesicle / protein monoubiquitination / Synthesis of PIPs at the plasma membrane / centriolar satellite / endoplasmic reticulum to Golgi vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / extrinsic component of cytoplasmic side of plasma membrane / Degradation of DVL / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / intracellular membrane-bounded organelle / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PKHA4-7, PH domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain ...PKHA4-7, PH domain / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / PH domain / SKP1/BTB/POZ domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Kelch-like protein 12 / Pleckstrin homology domain-containing family A member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsDalietou, E.V. / Chen, Z. / Ramdass, A.E. / Manning, C. / Richardson, W. / Aitmakhanova, K. / Platt, M. / Pike, A.C.W. / Fedorov, O. / Brennan, P. / Bullock, A.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008784/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the kelch domain of human KLHL12 in complex with PLEKHA4 peptide
Authors: Dalietou, E.V. / Chen, Z. / Ramdass, A.E. / Manning, C. / Richardson, W. / Aitmakhanova, K. / Platt, M. / Pike, A.C.W. / Fedorov, O. / Brennan, P. / Bullock, A.N.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 2.0Apr 17, 2024Group: Advisory / Atomic model / Structure summary
Category: atom_site / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues
Item: _atom_site.auth_seq_id / _atom_site.label_seq_id ..._atom_site.auth_seq_id / _atom_site.label_seq_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id
Revision 2.1Apr 24, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 12
B: Kelch-like protein 12
C: Kelch-like protein 12
D: Kelch-like protein 12
F: Pleckstrin homology domain-containing family A member 4
G: Pleckstrin homology domain-containing family A member 4
H: Pleckstrin homology domain-containing family A member 4
E: Pleckstrin homology domain-containing family A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,83817
Polymers135,4248
Non-polymers4159
Water7,008389
1
A: Kelch-like protein 12
E: Pleckstrin homology domain-containing family A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9183
Polymers33,8562
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-3 kcal/mol
Surface area11460 Å2
MethodPISA
2
B: Kelch-like protein 12
F: Pleckstrin homology domain-containing family A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1479
Polymers33,8562
Non-polymers2917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-19 kcal/mol
Surface area11750 Å2
MethodPISA
3
C: Kelch-like protein 12
G: Pleckstrin homology domain-containing family A member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9183
Polymers33,8562
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-5 kcal/mol
Surface area11570 Å2
MethodPISA
4
D: Kelch-like protein 12
H: Pleckstrin homology domain-containing family A member 4


Theoretical massNumber of molelcules
Total (without water)33,8562
Polymers33,8562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-10 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.469, 73.086, 103.734
Angle α, β, γ (deg.)90.000, 98.810, 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

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Protein / Protein/peptide , 2 types, 8 molecules ABCDFGHE

#1: Protein
Kelch-like protein 12 / / CUL3-interacting protein 1 / DKIR homolog / hDKIR


Mass: 32905.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHL12, C3IP1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53G59
#2: Protein/peptide
Pleckstrin homology domain-containing family A member 4 / PH domain-containing family A member 4 / Phosphoinositol 3-phosphate-binding protein 1 / PEPP-1


Mass: 950.004 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Pleckstrin homology domain-containing family A member 4 (PLEKHA4) 11-mer peptide
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H4M7

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Non-polymers , 4 types, 398 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M citrate pH 5.5, 0.4 M NaCl, 27,1% PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.954→79.52 Å / Num. obs: 86247 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 29.59 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.3
Reflection shellResolution: 1.954→1.988 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4299 / CC1/2: 0.309 / CC star: -0 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
XDSFeb 5, 2021 (BUILT 20210323)data reduction
STARANISO2.3.73 (20210329)data scaling
pointless1.12.10data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.954→79.52 Å / SU ML: 0.2992 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3873
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2486 4317 5.03 %
Rwork0.1996 81577 -
obs0.2021 85894 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.76 Å2
Refinement stepCycle: LAST / Resolution: 1.954→79.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8671 0 24 389 9084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718965
X-RAY DIFFRACTIONf_angle_d0.870912224
X-RAY DIFFRACTIONf_chiral_restr0.05861371
X-RAY DIFFRACTIONf_plane_restr0.00641572
X-RAY DIFFRACTIONf_dihedral_angle_d14.36573150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.954-1.980.36761310.34592631X-RAY DIFFRACTION96.14
1.98-20.4091290.35032598X-RAY DIFFRACTION96.5
2-2.020.38581440.33622682X-RAY DIFFRACTION98.67
2.02-2.050.39151390.32952707X-RAY DIFFRACTION98.92
2.05-2.080.3461610.31422647X-RAY DIFFRACTION99.43
2.08-2.110.35031540.28672712X-RAY DIFFRACTION99.58
2.11-2.140.31271460.28082725X-RAY DIFFRACTION99.79
2.14-2.170.30571390.28222699X-RAY DIFFRACTION99.89
2.17-2.20.30171430.26522711X-RAY DIFFRACTION99.96
2.2-2.240.34651440.26092743X-RAY DIFFRACTION99.9
2.24-2.280.30751360.23842692X-RAY DIFFRACTION99.96
2.28-2.320.29361530.23612719X-RAY DIFFRACTION99.9
2.32-2.360.30591510.23142745X-RAY DIFFRACTION100
2.36-2.410.29651340.23742695X-RAY DIFFRACTION100
2.41-2.460.28221440.23172725X-RAY DIFFRACTION99.93
2.46-2.520.29031480.22442754X-RAY DIFFRACTION99.97
2.52-2.580.26611340.22162710X-RAY DIFFRACTION99.96
2.58-2.650.26021730.20692681X-RAY DIFFRACTION99.96
2.65-2.730.27071520.20432720X-RAY DIFFRACTION99.93
2.73-2.820.22071240.21142767X-RAY DIFFRACTION99.97
2.82-2.920.29561480.19552703X-RAY DIFFRACTION99.93
2.92-3.040.26551330.20322738X-RAY DIFFRACTION99.83
3.04-3.170.24051370.20262738X-RAY DIFFRACTION100
3.17-3.340.24951210.18032781X-RAY DIFFRACTION99.86
3.34-3.550.25861430.18732718X-RAY DIFFRACTION99.9
3.55-3.830.23471330.17062771X-RAY DIFFRACTION99.97
3.83-4.210.19591650.14612722X-RAY DIFFRACTION99.97
4.21-4.820.16131540.12822735X-RAY DIFFRACTION99.97
4.82-6.070.17381520.15512784X-RAY DIFFRACTION99.86
6.07-79.520.2181520.18232824X-RAY DIFFRACTION99.5

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