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- PDB-6ttk: Crystal structure of the kelch domain of human KLHL12 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ttk
TitleCrystal structure of the kelch domain of human KLHL12 in complex with DVL1 peptide
Components
  • DVL1
  • Kelch-like protein 12
KeywordsLIGASE / Cullin3 E3 ligase / Kelch / Complex / Substrate peptide
Function / homology
Function and homology information


positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / neural crest formation / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / protein localization to microtubule ...positive regulation of protein localization to presynapse / Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / skeletal muscle acetylcholine-gated channel clustering / cochlea morphogenesis / neural crest formation / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / protein localization to microtubule / neural crest cell development / collateral sprouting / presynapse assembly / COPII vesicle coat / COPII vesicle coating / WNT5:FZD7-mediated leishmania damping / neurotransmitter secretion / dendritic spine morphogenesis / frizzled binding / axon extension / PCP/CE pathway / Wnt signalosome / WNT mediated activation of DVL / dendrite morphogenesis / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / neural tube development / regulation of postsynapse organization / clathrin-coated vesicle / regulation of synaptic vesicle exocytosis / Cul3-RING ubiquitin ligase complex / neuromuscular junction development / receptor clustering / COPII-coated ER to Golgi transport vesicle / heart looping / neuronal dense core vesicle / outflow tract morphogenesis / synaptic vesicle exocytosis / protein monoubiquitination / social behavior / positive regulation of excitatory postsynaptic potential / protein localization to nucleus / centriolar satellite / canonical Wnt signaling pathway / lateral plasma membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / prepulse inhibition / cytoplasmic microtubule organization / negative regulation of protein phosphorylation / TCF dependent signaling in response to WNT / RHO GTPases Activate Formins / axon guidance / Degradation of DVL / synapse organization / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / small GTPase binding / beta-catenin binding / Wnt signaling pathway / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / growth cone / cytoplasmic vesicle / microtubule / dendritic spine / postsynaptic density / protein stabilization / neuron projection / intracellular signal transduction / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / synapse / regulation of DNA-templated transcription / protein kinase binding / enzyme binding / positive regulation of transcription by RNA polymerase II / identical protein binding / cytosol
Similarity search - Function
Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Kelch-type beta propeller / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP 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 / 6 Propeller / Neuraminidase / SKP1/BTB/POZ domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Segment polarity protein dishevelled homolog DVL-1 / Kelch-like protein 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.383 Å
AuthorsChen, Z. / Williams, E. / Pike, A.C.W. / Strain-Damerell, C. / Wang, D. / Chalk, R. / Burgess-Brown, N. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. ...Chen, Z. / Williams, E. / Pike, A.C.W. / Strain-Damerell, C. / Wang, D. / Chalk, R. / Burgess-Brown, N. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N.
CitationJournal: Open Biology / Year: 2020
Title: Identification of a PGXPP degron motif in dishevelled and structural basis for its binding to the E3 ligase KLHL12.
Authors: Chen, Z. / Wasney, G.A. / Picaud, S. / Filippakopoulos, P. / Vedadi, M. / D'Angiolella, V. / Bullock, A.N.
History
DepositionDec 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 24, 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

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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: DVL1
G: DVL1
H: DVL1
E: DVL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,51114
Polymers137,3228
Non-polymers1896
Water11,620645
1
A: Kelch-like protein 12
E: DVL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4164
Polymers34,3312
Non-polymers852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-12 kcal/mol
Surface area11930 Å2
MethodPISA
2
B: Kelch-like protein 12
F: DVL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3764
Polymers34,3312
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-24 kcal/mol
Surface area11800 Å2
MethodPISA
3
C: Kelch-like protein 12
G: DVL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3533
Polymers34,3312
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-17 kcal/mol
Surface area11910 Å2
MethodPISA
4
D: Kelch-like protein 12
H: DVL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3663
Polymers34,3312
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-14 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.225, 73.145, 101.845
Angle α, β, γ (deg.)90.000, 94.500, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53G59
#2: Protein/peptide
DVL1


Mass: 1424.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O14640*PLUS

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Non-polymers , 4 types, 651 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 30% PEG4000, 0.2 M ammonium acetate, 0.1 M acetate pH 4.6

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.38→79.98 Å / Num. obs: 47109 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.83 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.107 / Rrim(I) all: 0.232 / Net I/σ(I): 5.8 / Num. measured all: 212254
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.38-2.514.50.7413110968600.8160.3880.842.299.7
7.54-79.984.40.095680315620.9890.0510.10810.299.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å79.98 Å
Translation2.4 Å79.98 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPJ

2vpj


Resolution: 2.383→79.978 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 2359 5.02 %
Rwork0.2253 44653 -
obs0.2266 47012 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.35 Å2 / Biso mean: 26.1151 Å2 / Biso min: 5.57 Å2
Refinement stepCycle: final / Resolution: 2.383→79.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8712 0 15 645 9372
Biso mean--24.58 27.53 -
Num. residues----1171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3834-2.43210.31831410.29062616100
2.4321-2.48490.36631140.2925261299
2.4849-2.54270.32291530.27692601100
2.5427-2.60630.26861190.27082639100
2.6063-2.67680.31751390.2634260099
2.6768-2.75560.2861320.25062625100
2.7556-2.84450.27331490.24522620100
2.8445-2.94620.23011320.23472612100
2.9462-3.06420.26861470.23332625100
3.0642-3.20360.26371150.22762647100
3.2036-3.37250.22231470.21462594100
3.3725-3.58380.2461290.22172627100
3.5838-3.86050.2111480.19832641100
3.8605-4.2490.22991550.19312632100
4.249-4.86380.21351480.18482622100
4.8638-6.12750.23431350.20712668100
6.1275-79.9780.2541560.2269267298

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