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- PDB-6m8r: Crystal structure of the KCTD16 BTB domain in complex with GABAB2... -

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Basic information

Entry
Database: PDB / ID: 6m8r
TitleCrystal structure of the KCTD16 BTB domain in complex with GABAB2 peptide
Components
  • BTB/POZ domain-containing protein KCTD16
  • Gamma-aminobutyric acid type B receptor subunit 2
KeywordsPROTEIN BINDING / pentamer / BTB domain
Function / homology
Function and homology information


GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / regulation of G protein-coupled receptor signaling pathway / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic ...GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / regulation of G protein-coupled receptor signaling pathway / negative regulation of adenylate cyclase activity / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / transmembrane signaling receptor activity / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / receptor complex / neuron projection / protein heterodimerization activity / G protein-coupled receptor signaling pathway / plasma membrane / cytoplasm
Similarity search - Function
: / GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, GABA-B receptor / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 ...: / GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / GPCR family 3, GABA-B receptor / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR, family 3 / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid type B receptor subunit 2 / BTB/POZ domain-containing protein KCTD16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsZheng, S. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateKlingenstein-Simons Fellowship United States
CitationJournal: Nature / Year: 2019
Title: Structural basis for KCTD-mediated rapid desensitization of GABABsignalling.
Authors: Zheng, S. / Abreu, N. / Levitz, J. / Kruse, A.C.
History
DepositionAug 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: 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

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Assembly

Deposited unit
G: BTB/POZ domain-containing protein KCTD16
H: BTB/POZ domain-containing protein KCTD16
I: BTB/POZ domain-containing protein KCTD16
J: BTB/POZ domain-containing protein KCTD16
B: BTB/POZ domain-containing protein KCTD16
C: BTB/POZ domain-containing protein KCTD16
D: BTB/POZ domain-containing protein KCTD16
E: BTB/POZ domain-containing protein KCTD16
A: BTB/POZ domain-containing protein KCTD16
F: BTB/POZ domain-containing protein KCTD16
K: Gamma-aminobutyric acid type B receptor subunit 2
L: Gamma-aminobutyric acid type B receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,29014
Polymers131,24112
Non-polymers492
Water00
1
G: BTB/POZ domain-containing protein KCTD16
H: BTB/POZ domain-containing protein KCTD16
I: BTB/POZ domain-containing protein KCTD16
J: BTB/POZ domain-containing protein KCTD16
F: BTB/POZ domain-containing protein KCTD16
K: Gamma-aminobutyric acid type B receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6457
Polymers65,6216
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-36 kcal/mol
Surface area23990 Å2
MethodPISA
2
B: BTB/POZ domain-containing protein KCTD16
C: BTB/POZ domain-containing protein KCTD16
D: BTB/POZ domain-containing protein KCTD16
E: BTB/POZ domain-containing protein KCTD16
A: BTB/POZ domain-containing protein KCTD16
L: Gamma-aminobutyric acid type B receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6457
Polymers65,6216
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-34 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.964, 64.945, 114.137
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BTB/POZ domain-containing protein KCTD16 / Potassium channel tetramerization domain-containing protein 16


Mass: 12220.125 Da / Num. of mol.: 10 / Fragment: UNP residues 23-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD16, KIAA1317
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q68DU8
#2: Protein/peptide Gamma-aminobutyric acid type B receptor subunit 2 / Gb2 / G-protein coupled receptor 51 / HG20


Mass: 4520.067 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR2, GPR51, GPRC3B
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O75899
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM magnesium chloride, 100 mM Tris-HCl, pH 7.5, 12% w/v PEG8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2017
RadiationMonochromator: double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 22162 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.926 / Rmerge(I) obs: 0.332 / Rpim(I) all: 0.208 / Rrim(I) all: 0.394 / Net I/σ(I): 3.4
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1073 / CC1/2: 0.561 / Rpim(I) all: 0.703 / Rrim(I) all: 1.226 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5A15

5a15


Resolution: 3.2→38.639 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1686 7.66 %
Rwork0.2171 --
obs0.2208 22002 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→38.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8576 0 2 0 8578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038829
X-RAY DIFFRACTIONf_angle_d0.63711939
X-RAY DIFFRACTIONf_dihedral_angle_d13.2655251
X-RAY DIFFRACTIONf_chiral_restr0.0451282
X-RAY DIFFRACTIONf_plane_restr0.0061525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29410.34411320.30151604X-RAY DIFFRACTION95
3.2941-3.40040.33721380.26831664X-RAY DIFFRACTION98
3.4004-3.52190.2821390.25521671X-RAY DIFFRACTION98
3.5219-3.66280.33231380.24721672X-RAY DIFFRACTION99
3.6628-3.82930.26781430.23351713X-RAY DIFFRACTION99
3.8293-4.0310.26731380.20721671X-RAY DIFFRACTION100
4.031-4.28330.28271400.20311683X-RAY DIFFRACTION99
4.2833-4.61350.24941410.19641696X-RAY DIFFRACTION99
4.6135-5.07680.22071420.18731701X-RAY DIFFRACTION100
5.0768-5.80930.25081430.19651724X-RAY DIFFRACTION100
5.8093-7.3110.25861430.22981734X-RAY DIFFRACTION100
7.311-38.64180.22771490.19551783X-RAY DIFFRACTION100

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