[English] 日本語
Yorodumi
- EMDB-36902: Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic aci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36902
TitleCryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 (Local refinement)
Map datasharpening map
Sample
  • Complex: GSK256073 bound human hydroxy-carboxylic acid receptor 2
    • Protein or peptide: Human hydroxycarboxylic acid receptor 2
  • Ligand: 8-chloranyl-3-pentyl-7H-purine-2,6-dione
KeywordsGPCR / G-Protein / MEMBRANE PROTEIN / signaling
Function / homology
Function and homology information


nicotinic acid receptor activity / Hydroxycarboxylic acid-binding receptors / neutrophil apoptotic process / Class A/1 (Rhodopsin-like receptors) / positive regulation of neutrophil apoptotic process / positive regulation of adiponectin secretion / negative regulation of lipid catabolic process / cell junction / G alpha (i) signalling events / G protein-coupled receptor signaling pathway / plasma membrane
Similarity search - Function
G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Hydroxycarboxylic acid receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsPark JH / Ishimoto N / Park SY
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2
Authors: Park JH / Kawakami K / Ishimoto N / Ikuta T / Ohki M / Ekimoto T / Ikeguchi M / Lee DS / Lee YH / Tame JRH / Inoue A / Park SY
History
DepositionJul 21, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_36902.png

Downloads & links

-
Map

FileDownload / File: emd_36902.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpening map
Voxel sizeX=Y=Z: 1.245 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.4055184 - 1.7348868
Average (Standard dev.)-0.00061460555 (±0.030790929)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_36902_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: map

Fileemd_36902_additional_1.map
Annotationmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2

Fileemd_36902_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1

Fileemd_36902_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GSK256073 bound human hydroxy-carboxylic acid receptor 2

EntireName: GSK256073 bound human hydroxy-carboxylic acid receptor 2
Components
  • Complex: GSK256073 bound human hydroxy-carboxylic acid receptor 2
    • Protein or peptide: Human hydroxycarboxylic acid receptor 2
  • Ligand: 8-chloranyl-3-pentyl-7H-purine-2,6-dione

-
Supramolecule #1: GSK256073 bound human hydroxy-carboxylic acid receptor 2

SupramoleculeName: GSK256073 bound human hydroxy-carboxylic acid receptor 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 KDa

-
Macromolecule #1: Human hydroxycarboxylic acid receptor 2

MacromoleculeName: Human hydroxycarboxylic acid receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.320297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH ...String:
GPGAPADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKV KEAQAAAEQL KTTRNAYIQK YLEFMNRHHL QDHFLEIDKK NCCVFRDDFI VKVLPPVLGL EFIFGLLGNG L ALWIFCFH LKSWKSSRIF LFNLAVADFL LIICLPFLMD NYVRRWDWKF GDIPCRLMLF MLAMNRQGSI IFLTVVAVDR YF RVVHPHH ALNKISNRTA AIISCLLWGI TIGLTVHLLK KKMPIQNGGA NLCSSFSICH TFQWHEAMFL LEFFLPLGII LFC SARIIW SLRQRQMDRH AKIKRAITFI MVVAIVFVIC FLPSVVVRIR IFWLLHTSGT QNCEVYRSVD LAFFITLSFT YMNS MLDPV VYYFSSPSFP NFFSTLINRC LQRKMTGEPD NNRSTSVELT GDPNKTRGAP EALMANSGEP WSPSYLGPTS P

UniProtKB: Hydroxycarboxylic acid receptor 2

-
Macromolecule #2: 8-chloranyl-3-pentyl-7H-purine-2,6-dione

MacromoleculeName: 8-chloranyl-3-pentyl-7H-purine-2,6-dione / type: ligand / ID: 2 / Number of copies: 1 / Formula: OKL
Molecular weightTheoretical: 256.689 Da
Chemical component information

ChemComp-OKL:
8-chloranyl-3-pentyl-7H-purine-2,6-dione

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 5434103
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 153633
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8k5d:
Cryo-EM structure of GSK256073 bound human hydroxy-carboxylic acid receptor 2 (Local refinement)

+
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