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- PDB-6m8s: Crystal structure of the KCTD12 H1 domain in complex with Gbeta1g... -

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Basic information

Entry
Database: PDB / ID: 6m8s
TitleCrystal structure of the KCTD12 H1 domain in complex with Gbeta1gamma2 subunits
Components
  • BTB/POZ domain-containing protein KCTD12
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsSIGNALING PROTEIN / beta-propeller / homopentamer / GABAB desensitization
Function / homology
Function and homology information


regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels ...regulation of G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / presynaptic membrane / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Ras protein signal transduction / postsynaptic membrane / Extra-nuclear estrogen signaling / cell population proliferation / receptor complex / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / KCTD8/12/16 H1 domain / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase ...: / KCTD8/12/16 H1 domain / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / BTB/POZ domain-containing protein KCTD12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.71 Å
AuthorsZheng, S. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateKlingenstein-Simons Fellowship Program 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

Downloads & links

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Assembly

Deposited unit
C: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
D: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
H: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
I: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
J: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
K: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
L: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
A: BTB/POZ domain-containing protein KCTD12
O: BTB/POZ domain-containing protein KCTD12
P: BTB/POZ domain-containing protein KCTD12
B: BTB/POZ domain-containing protein KCTD12
E: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
F: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
M: BTB/POZ domain-containing protein KCTD12


Theoretical massNumber of molelcules
Total (without water)304,88615
Polymers304,88615
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, microscopy, Negative stain electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47020 Å2
ΔGint-257 kcal/mol
Surface area93840 Å2
Unit cell
Length a, b, c (Å)109.090, 121.990, 206.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38534.062 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#2: Protein
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7845.078 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768
#3: Protein
BTB/POZ domain-containing protein KCTD12 / Pfetin / Predominantly fetal expressed T1 domain


Mass: 14598.107 Da / Num. of mol.: 5 / Fragment: UNP residues 200-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD12, C13orf2, KIAA1778, PFET1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q96CX2

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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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 8% 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: Apr 19, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.71→50 Å / Num. obs: 29623 / % possible obs: 99 % / Redundancy: 3.9 % / Net I/σ(I): 3.56
Reflection shellResolution: 3.71→3.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2129 / CC1/2: 0.52 / Rrim(I) all: 1.213 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OMW

1omw


Resolution: 3.71→48.406 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 3705 6.75 %
Rwork0.2508 --
obs0.2533 29596 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.71→48.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18981 0 0 0 18981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00319331
X-RAY DIFFRACTIONf_angle_d0.70626166
X-RAY DIFFRACTIONf_dihedral_angle_d14.00711487
X-RAY DIFFRACTIONf_chiral_restr0.0462931
X-RAY DIFFRACTIONf_plane_restr0.0063379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.71-3.75880.42821390.37711959X-RAY DIFFRACTION97
3.7588-3.81030.38071430.33332003X-RAY DIFFRACTION99
3.8103-3.86470.31430.32541959X-RAY DIFFRACTION99
3.8647-3.92240.3571510.31452015X-RAY DIFFRACTION99
3.9224-3.98360.36091470.31891992X-RAY DIFFRACTION99
3.9836-4.04890.34771480.30912010X-RAY DIFFRACTION99
4.0489-4.11870.35441430.31141964X-RAY DIFFRACTION99
4.1187-4.19360.37091460.29392020X-RAY DIFFRACTION98
4.1936-4.27420.3191410.28821957X-RAY DIFFRACTION98
4.2742-4.36140.30161460.28542007X-RAY DIFFRACTION98
4.3614-4.45610.29441400.23721913X-RAY DIFFRACTION97
4.4561-4.55970.29061440.24042000X-RAY DIFFRACTION97
4.5597-4.67360.26461380.2281944X-RAY DIFFRACTION97
4.6736-4.79990.2611400.23891919X-RAY DIFFRACTION95
4.7999-4.9410.25881420.2281935X-RAY DIFFRACTION96
4.941-5.10030.29041350.2231944X-RAY DIFFRACTION95
5.1003-5.28240.26081400.24181921X-RAY DIFFRACTION95
5.2824-5.49360.30221370.25431921X-RAY DIFFRACTION96
5.4936-5.74330.331430.26361984X-RAY DIFFRACTION98
5.7433-6.04550.31041430.25982011X-RAY DIFFRACTION99
6.0455-6.42350.28981460.24671976X-RAY DIFFRACTION98
6.4235-6.91820.23521390.21541982X-RAY DIFFRACTION98
6.9182-7.6120.28741460.2271992X-RAY DIFFRACTION98
7.612-8.70790.2251370.19971937X-RAY DIFFRACTION96
8.7079-10.950.19091460.16921928X-RAY DIFFRACTION95
10.95-48.40990.25141420.23241956X-RAY DIFFRACTION97

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