[English] 日本語
Yorodumi
- PDB-6m8r: Crystal structure of the KCTD16 BTB domain in complex with GABAB2... -

+
Open data


ID or keywords:

Loading...

-
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 / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / neuron-glial cell signaling / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway ...GABA B receptor activation / G protein-coupled GABA receptor complex / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / neuron-glial cell signaling / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / behavioral fear response / cell projection / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / protein homooligomerization / memory / 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 / G protein-coupled receptor signaling pathway / protein heterodimerization activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / KCTD8/12/16 H1 domain / 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 / G-protein coupled receptors family 3 signature 3. / Potassium Channel Kv1.1; Chain A ...: / KCTD8/12/16 H1 domain / 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 / G-protein coupled receptors family 3 signature 3. / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / GPCR, family 3, conserved site / GPCR, family 3 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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