[English] 日本語
Yorodumi
- EMDB-63683: Cryo-EM structure of the orphan receptor GPRC5D in ligand free st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63683
TitleCryo-EM structure of the orphan receptor GPRC5D in ligand free state resolved via the fusion/crosslinking strategy
Map data
Sample
  • Complex: Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex
    • Protein or peptide: G-protein coupled receptor family C group 5 member D
    • Protein or peptide: GFP-clamp E186C
    • Protein or peptide: Green fluorescent protein
  • Ligand: CHOLESTEROL
KeywordsOrphan receptor GPRC5D / Fusion/crosslinking strategy / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein kinase activator activity / bioluminescence / generation of precursor metabolites and energy / G protein-coupled receptor activity / signaling receptor complex / extracellular exosome / plasma membrane
Similarity search - Function
: / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / G protein-coupled receptor family C group 5 member D
Similarity search - Component
Biological speciesHomo sapiens (human) / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsHan SC / Li MH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure determination of GPCRs with disulfide-crosslinked fusion protein
Authors: Han SC / Li MH
History
DepositionMar 10, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63683.png

Downloads & links

-
Map

FileDownload / File: emd_63683.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-5.6930776 - 7.3549223
Average (Standard dev.)-0.0013827538 (±0.10831576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_63683_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63683_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex

EntireName: Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex
Components
  • Complex: Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex
    • Protein or peptide: G-protein coupled receptor family C group 5 member D
    • Protein or peptide: GFP-clamp E186C
    • Protein or peptide: Green fluorescent protein
  • Ligand: CHOLESTEROL

-
Supramolecule #1: Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex

SupramoleculeName: Apo GPRC5D-GFP10-11:GFP1-9:GFP-clamp E186C complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: G-protein coupled receptor family C group 5 member D

MacromoleculeName: G-protein coupled receptor family C group 5 member D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.651039 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YKDCIESTGD YFLLCDAEGP WGIILESLAI LGIVVTILLL LAFLFLMRKI QDCSQWNVLP TQLLFLLSVL GLFGLAFAFI IELNQQTAP VRYFLFGVLF ALCFSCLLAH ASNLVKLVRG CVSFSWTTIL CIAIGCSLLQ IIIATEYVTL IMTRGMMFVN M TPCQLNVD ...String:
YKDCIESTGD YFLLCDAEGP WGIILESLAI LGIVVTILLL LAFLFLMRKI QDCSQWNVLP TQLLFLLSVL GLFGLAFAFI IELNQQTAP VRYFLFGVLF ALCFSCLLAH ASNLVKLVRG CVSFSWTTIL CIAIGCSLLQ IIIATEYVTL IMTRGMMFVN M TPCQLNVD FVVLLVYVLF LMALTFFVSK ATFCGPRRQL GHYLSTQTSL SKDLNEKRDH MVLLEFVTAA GLQKEKQHGR LI FITVLFS IIIWVVWISM LLRGNPQFQR QPQWDDPVVC IALVTNAWVF LLLYIVPELC ILYRSCRQEC PLQGNACPVT AYQ HSFQVE NQELSRARDS DGAEEDVALT SYGTPIQPQT VDPTQECFIP QAKLSPQQDA GGV

UniProtKB: G protein-coupled receptor family C group 5 member D, G protein-coupled receptor family C group 5 member D

-
Macromolecule #2: Green fluorescent protein

MacromoleculeName: Green fluorescent protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 22.388293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTRKGEELF TGVVPILIEL DGDVNGHKFS VRGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTL(CRO)VQC FSRYPD HMK RHDFFKSAMP EGYVQERTIY FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYIMADK QN NGIKANFKIR ...String:
MGTRKGEELF TGVVPILIEL DGDVNGHKFS VRGEGEGDAT YGKLTLKFIC TTGKLPVPWP TLVTTL(CRO)VQC FSRYPD HMK RHDFFKSAMP EGYVQERTIY FKDDGTYKTR AEVKFEGDTL VNRIELKGID FKEDGNILGH KLEYNFNSHN VYIMADK QN NGIKANFKIR HNVEDGSVQL ADHYQQNTPI GDGPVLLP

UniProtKB: Green fluorescent protein

-
Macromolecule #3: GFP-clamp E186C

MacromoleculeName: GFP-clamp E186C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.038664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DLGKKLLEAA RAGQDDEVRI LMANGADVNA ADDVGVTPLH LAAQRGHLEI VEVLLKYGAD VNAADLWGQT PLHLAATAGH LEIVEVLLK NGADVNARDN IGHTPLHLAA WAGHLEIVEV LLKYGADVNA QDKFGKTPFD LAIDNGNEDI AEVLQKAAGG G SGGGDVNA ...String:
DLGKKLLEAA RAGQDDEVRI LMANGADVNA ADDVGVTPLH LAAQRGHLEI VEVLLKYGAD VNAADLWGQT PLHLAATAGH LEIVEVLLK NGADVNARDN IGHTPLHLAA WAGHLEIVEV LLKYGADVNA QDKFGKTPFD LAIDNGNEDI AEVLQKAAGG G SGGGDVNA YDEVGWTPLH KAAWGHLCKV EDLLKNGADV NAADIDGYTP LHLAAFSGHL EIVEVLLKYG ADVNADDQAG FT PLHLAAI FGHLEIVEVL LKNGADVNAQ DKFGKTPFDL AIDNGNEDIA EVLQKAA

-
Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 177987
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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