[English] 日本語
Yorodumi
- EMDB-61742: CGP54626-bound-DGABAB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61742
TitleCGP54626-bound-DGABAB
Map data
Sample
  • Complex: Drosophila metabotropic GABA-B receptor
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
    • Protein or peptide: Metabotropic GABA-B receptor subtype 1
  • Ligand: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
KeywordsCOMPLEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of synaptic vesicle fusion to presynaptic active zone membrane / olfactory behavior / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / cellular response to mechanical stimulus / negative regulation of insulin secretion / 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 / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Metabotropic GABA-B receptor subtype 2 / Metabotropic GABA-B receptor subtype 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
Authorsshen CS / liu JF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of GABAB receptor activation during evolution
Authors: shen CS / liu JF
History
DepositionSep 28, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61742.png

Downloads & links

-
Map

FileDownload / File: emd_61742.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 280 pix.
= 260.4 Å		0.93 Å/pix.
x 280 pix.
= 260.4 Å		0.93 Å/pix.
x 280 pix.
= 260.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.172
Minimum - Maximum-0.23202993 - 1.2414906
Average (Standard dev.)0.0073956205 (±0.028820898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 260.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61742_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61742_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61742_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Drosophila metabotropic GABA-B receptor

EntireName: Drosophila metabotropic GABA-B receptor
Components
  • Complex: Drosophila metabotropic GABA-B receptor
    • Protein or peptide: Gamma-aminobutyric acid type B receptor subunit 2
    • Protein or peptide: Metabotropic GABA-B receptor subtype 1
  • Ligand: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid

-
Supramolecule #1: Drosophila metabotropic GABA-B receptor

SupramoleculeName: Drosophila metabotropic GABA-B receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 200 kDa/nm

-
Macromolecule #1: Metabotropic GABA-B receptor subtype 1

MacromoleculeName: Metabotropic GABA-B receptor subtype 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 79.778414 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELHIGGIFPI AGKGGWQGGQ ACMPATRLAL DDVNKQPNLL PGFKLILHSN DSECEPGLGA SVMYNLLYNK PQKLMLLAGC STVCTTVAE AAKMWNLIVL CYGASSPALS DRKRFPTLFR THPSATVHNP TRIKLMKKFG WSRVAILQQA EEVFISTVED L ENRCMEAG ...String:
ELHIGGIFPI AGKGGWQGGQ ACMPATRLAL DDVNKQPNLL PGFKLILHSN DSECEPGLGA SVMYNLLYNK PQKLMLLAGC STVCTTVAE AAKMWNLIVL CYGASSPALS DRKRFPTLFR THPSATVHNP TRIKLMKKFG WSRVAILQQA EEVFISTVED L ENRCMEAG VEIVTRQSFL SDPTDAVRNL RRQDARIIVG LFYVVAARRV LCEMYKQQLY GRAHVWFFIG WYEDNWYEVN LK AEGITCT VEQMRIAAEG HLTTEALMWN QNNQTTISGM TAEEFRHRLN QALIEEGYDI NHDRYPEGYQ EAPLAYDAVW SVA LAFNKT MERLTTGKKS LRDFTYTDKE IADEIYAAMN STQFLGVSGV VAFSSQGDRI ALTQIEQMID GKYEKLGYYD TQLD NLSWL NTEQWIGGKV PQDRTIVTHV LRTVSLPLFV CMCTISSCGI FVAFALIIFN IWNKHRRVIQ SSHPVCNTIM LFGVI ICLI SVILLGIDGR FVSPEEYPKI CQARAWLLST GFTLAYGAMF SKVWRVHRFT TKAKTDPKKK VEPWKLYTMV SGLLSI DLV ILLSWQIFDP LQRYLETFPL EDPVSTTDDI KIRPELEHCE SQRNSMWLGL VYGFKGLILV FGLFLAYETR SIKVKQI ND SRYVGMSIYN VVVLCLITAP VGMVIASQQD ASFAFVALAV IFCCFLSMLL IFVPKVIEVI RH

UniProtKB: Metabotropic GABA-B receptor subtype 1

-
Macromolecule #2: Gamma-aminobutyric acid type B receptor subunit 2

MacromoleculeName: Gamma-aminobutyric acid type B receptor subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 87.493703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RTAKRSDVYI AGFFPYGDGV ENSYTGRGVM PSVKLALGHV NEHGKILANY RLHMWWNDTQ CNAAVGVKSF FDMMHSGPNK VMLFGAACT HVTDPIAKAS KHWHLTQLSY ADTHPMFTKD AFPNFFRVVP SENAFNAPRL ALLKEFNWTR VGTVYQNEPR Y SLPHNHMV ...String:
RTAKRSDVYI AGFFPYGDGV ENSYTGRGVM PSVKLALGHV NEHGKILANY RLHMWWNDTQ CNAAVGVKSF FDMMHSGPNK VMLFGAACT HVTDPIAKAS KHWHLTQLSY ADTHPMFTKD AFPNFFRVVP SENAFNAPRL ALLKEFNWTR VGTVYQNEPR Y SLPHNHMV ADLDAMEVEV VETQSFVNDV AESLKKLREK DVRIILGNFN EHFARKAFCE AYKLDMYGRA YQWLIMATYS TD WWNVTQD SECSVEEIAT ALEGAILVDL LPLSTSGDIT VAGITADEYL VEYDRLRGTE YSRFHGYTYD GIWAAALAIQ YVA EKREDL LTHFDYRVKD WESVFLEALR NTSFEGVTGP VRFYNNERKA NILINQFQLG QMEKIGEYHS QKSHLDLSLG KPVK WVGKT PPKDRTLIYI EHSQVNPTIY IVSASASVIG VIIATVFLAF NIKYRNQRYI KMSSPHLNNL IIVGCMITYL SIIFL GLDT TLSSVAAFPY ICTARAWILM AGFSLSFGAM FSKTWRVHSI FTDLKLNKKV IKDYQLFMVV GVLLAIDIAI ITTWQI ADP FYRETKQLEP LHHENIDDVL VIPENEYCQS EHMTIFVSII YAYKGLLLVF GAFLAWETRH VSIPALNDSK HIGFSVY NV FITCLAGAAI SLVLSDRKDL VFVLLSFFII FCTTATLCLV FVPKLVELKR NPQGVVDKRV RATLRPMSKN GRRDSSVC E LEQRLRDVKN TNCRFRKALM EKENELQALI RKLGPEARKW IDGVTC

UniProtKB: Metabotropic GABA-B receptor subtype 2

-
Macromolecule #3: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]...

MacromoleculeName: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
type: ligand / ID: 3 / Number of copies: 1 / Formula: 2BV
Molecular weightTheoretical: 408.3 Da
Chemical component information

ChemComp-2BV:
(R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 7.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 36119
Initial angle assignmentType: OTHER
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9jqx:
CGP54626-bound-DGABAB

+
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