[English] 日本語
Yorodumi
- PDB-6m8s: Crystal structure of the KCTD12 H1 domain in complex with Gbeta1g... -

+
Open data


ID or keywords:

Loading...

-
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


cell projection / 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 / protein homooligomerization / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels ...cell projection / 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 / protein homooligomerization / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / GTPase binding / presynaptic membrane / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / postsynaptic membrane / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / SKP1/BTB/POZ domain superfamily ...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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / SKP1/BTB/POZ domain superfamily / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Few Secondary Structures / Irregular / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more