[English] 日本語
Yorodumi
- PDB-5gwm: Solution structure of heterodimeric coiled-coil domain of Drosoph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gwm
TitleSolution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 3
Components
  • Metabotropic GABA-B receptor subtype 1
  • Metabotropic GABA-B receptor subtype 3, isoform A
KeywordsSIGNALING PROTEIN / GABAB receptor / Drosophila / coiled-coil
Function / homology
Function and homology information


G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / sleep / gamma-aminobutyric acid signaling pathway / transmembrane signaling receptor activity / membrane => GO:0016020 / G protein-coupled receptor signaling pathway / membrane
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR, family 3 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic GABA-B receptor subtype 1 / Metabotropic GABA-B receptor subtype 3, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, X. / Zhang, S. / Zhang, C.X. / Liu, J.
CitationJournal: To Be Published
Title: Solution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 3
Authors: Liu, X. / Zhang, S. / Zhang, C.X. / Liu, J.
History
DepositionSep 12, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metabotropic GABA-B receptor subtype 1
B: Metabotropic GABA-B receptor subtype 3, isoform A


Theoretical massNumber of molelcules
Total (without water)12,2822
Polymers12,2822
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area8470 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

-
Components

#1: Protein Metabotropic GABA-B receptor subtype 1


Mass: 6327.121 Da / Num. of mol.: 1 / Fragment: coiled-coil domain, UNP residues 751-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R1, CG15274 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9BML7
#2: Protein/peptide Metabotropic GABA-B receptor subtype 3, isoform A / GABAB receptor 3 / Metabotropic GABA-B receptor subtype 3 / isoform D / isoform E / isoform G


Mass: 5954.819 Da / Num. of mol.: 1 / Fragment: coiled-coil domain, UNP residues 914-954
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R3, CG3022, Dmel_CG3022 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9VPS7

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
132isotropic12D 1H-15N HSQC
142isotropic12D 1H-13C HSQC
152isotropic13D HNCO
1132isotropic13D HN(CA)CB
1142isotropic13D CBCA(CO)NH
1122isotropic13D HBHA(CO)NH
1112isotropic13D (H)CCH-TOCSY
1102isotropic13D 1H-13C NOESY
172isotropic13D C(CO)NH

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM PBS, 100 mM sodium chloride, 0.02 mg/mL sodium azide, 0.7 mM [U-99% 15N] Molecule1, 0.7 mM [U-99% 15N] Molecule2, 90% H2O/10% D2ON_sample90% H2O/10% D2O
solution220 mM PBS, 100 mM sodium chloride, 0.02 mg/mL sodium azide, 0.7 mM [U-99% 13C; U-99% 15N] Molecule1, 0.7 mM [U-99% 13C; U-99% 15N] Molecule2, 90% H2O/10% D2OCN_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMPBSnatural abundance1
100 mMsodium chloridenatural abundance1
0.02 mg/mLsodium azidenatural abundance1
0.7 mMMolecule1[U-99% 15N]1
0.7 mMMolecule2[U-99% 15N]1
20 mMPBSnatural abundance2
100 mMsodium chloridenatural abundance2
0.02 mg/mLsodium azidenatural abundance2
0.7 mMMolecule1[U-99% 13C; U-99% 15N]2
0.7 mMMolecule2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 120 mM / Label: condition1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

-
NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNMR2.3CCPNchemical shift assignment
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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