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- PDB-5nkp: Crystal structure of the human KLHL3 Kelch domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 5nkp
TitleCrystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide
Components
  • Kelch-like protein 3
  • Serine/threonine-protein kinase WNK3
KeywordsTRANSFERASE / Kelch domain
Function / homology
Function and homology information


distal tubule morphogenesis / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / renal sodium ion absorption / regulation of calcium ion import / positive regulation of sodium ion transport / potassium ion homeostasis / osmosensory signaling pathway ...distal tubule morphogenesis / positive regulation of ion transmembrane transporter activity / negative regulation of pancreatic juice secretion / positive regulation of sodium ion transmembrane transporter activity / monoatomic ion homeostasis / renal sodium ion absorption / regulation of calcium ion import / positive regulation of sodium ion transport / potassium ion homeostasis / osmosensory signaling pathway / positive regulation of calcium ion transport / cellular hyperosmotic response / membraneless organelle assembly / cell volume homeostasis / regulation of monoatomic cation transmembrane transport / positive regulation of peptidyl-threonine phosphorylation / Cul3-RING ubiquitin ligase complex / maintenance of blood-brain barrier / cullin family protein binding / bicellular tight junction / negative regulation of protein localization to plasma membrane / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / peptidyl-threonine phosphorylation / protein localization to plasma membrane / adherens junction / positive regulation of protein localization to plasma membrane / macroautophagy / molecular condensate scaffold activity / Stimuli-sensing channels / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / actin binding / ubiquitin-dependent protein catabolic process / protein autophosphorylation / gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / negative regulation of apoptotic process / structural molecule activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
Kelch-like protein 3 / : / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Kelch-type beta propeller / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch ...Kelch-like protein 3 / : / Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Kelch-type beta propeller / 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. / 6 Propeller / Neuraminidase / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Serine/threonine-protein kinase WNK3 / Kelch-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsChen, Z. / Sorrell, F.J. / Pinkas, D.M. / Williams, E. / Mathea, S. / Goubin, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Burgess-Brown, N. ...Chen, Z. / Sorrell, F.J. / Pinkas, D.M. / Williams, E. / Mathea, S. / Goubin, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Burgess-Brown, N. / Bountra, C. / Bullock, A.
CitationJournal: To Be Published
Title: Crystal structure of the human KLHL3 Kelch domain in complex with a WNK3 peptide
Authors: Chen, Z. / Sorrell, F.J. / Pinkas, D.M. / Williams, E. / Mathea, S. / Goubin, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Burgess-Brown, N. / Bountra, C. / Bullock, A.
History
DepositionMar 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch-like protein 3
B: Kelch-like protein 3
D: Serine/threonine-protein kinase WNK3
C: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9948
Polymers65,6964
Non-polymers2984
Water77543
1
A: Kelch-like protein 3
D: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1115
Polymers32,8482
Non-polymers2633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-23 kcal/mol
Surface area11690 Å2
MethodPISA
2
B: Kelch-like protein 3
C: Serine/threonine-protein kinase WNK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8833
Polymers32,8482
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 169.720, 123.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-549-

CYS

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Components

#1: Protein Kelch-like protein 3


Mass: 31529.459 Da / Num. of mol.: 2 / Fragment: UNP residues 298-587
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/peptide Serine/threonine-protein kinase WNK3 / Protein kinase lysine-deficient 3 / Protein kinase with no lysine 3


Mass: 1318.342 Da / Num. of mol.: 2 / Fragment: UNP residues 537-547 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9BYP7, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 6% PEG4K -- 0.1M acetate pH 5.1

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→50.03 Å / Num. obs: 22387 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 44.29 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.387 / Rpim(I) all: 0.109 / Rrim(I) all: 0.403 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.8713.62.2052236116420.490.6152.291.4100
12.52-50.0311.30.0633142930.9990.0190.0633098.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å50.03 Å
Translation2.8 Å50.03 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.26data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CH9

4ch9


Resolution: 2.8→50.025 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.62
RfactorNum. reflection% reflection
Rfree0.2472 1101 4.92 %
Rwork0.2288 --
obs0.2298 22358 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.34 Å2 / Biso mean: 38.0573 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.8→50.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 21 43 4558
Biso mean--43.81 37.51 -
Num. residues----596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134597
X-RAY DIFFRACTIONf_angle_d1.1296250
X-RAY DIFFRACTIONf_chiral_restr0.346685
X-RAY DIFFRACTIONf_plane_restr0.003820
X-RAY DIFFRACTIONf_dihedral_angle_d19.0531614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.92740.36531480.322426072755
2.9274-3.08170.30811410.302626072748
3.0817-3.27480.34971340.292626462780
3.2748-3.52760.29491450.267326172762
3.5276-3.88250.25341340.233826282762
3.8825-4.4440.2091210.191726772798
4.444-5.59770.19221360.176226902826
5.5977-50.0330.19261420.202427852927
Refinement TLS params.Method: refined / Origin x: 19.2051 Å / Origin y: 26.2355 Å / Origin z: 2.1074 Å
111213212223313233
T0.387 Å20.0089 Å2-0.0144 Å2-0.385 Å20.0346 Å2--0.4243 Å2
L0.8169 °20.3411 °20.6158 °2-0.4362 °20.7135 °2--1.3343 °2
S0.0876 Å °-0.0793 Å °-0.0882 Å °0.1215 Å °-0.0196 Å °-0.0258 Å °0.2361 Å °0.0327 Å °-0.0801 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA300 - 585
2X-RAY DIFFRACTION1allB297 - 585
3X-RAY DIFFRACTION1allD537 - 546
4X-RAY DIFFRACTION1allC537 - 547
5X-RAY DIFFRACTION1allE1 - 61
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allG2
9X-RAY DIFFRACTION1allG3

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