[English] 日本語
Yorodumi
- EMDB-60993: Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60993
TitleCryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex
Map data
Sample
  • Complex: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
    • Protein or peptide: G-protein coupled receptor 55,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Light chain
    • Protein or peptide: anti-Fab Nanobody
  • Ligand: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide
KeywordsGPCR / G protein / cryo-EM / membrane protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


cannabinoid receptor activity / Class A/1 (Rhodopsin-like receptors) / positive regulation of Rho protein signal transduction / negative regulation of osteoclast differentiation / bone resorption / electron transport chain / G protein-coupled receptor activity / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space ...cannabinoid receptor activity / Class A/1 (Rhodopsin-like receptors) / positive regulation of Rho protein signal transduction / negative regulation of osteoclast differentiation / bone resorption / electron transport chain / G protein-coupled receptor activity / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / G-protein coupled receptor 55
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHua T / Liu ZJ / Cherezov V / Chang H / Li XT / Shen L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91953202 China
CitationJournal: Cell Res / Year: 2025
Title: Structure basis of ligand recognition and activation of GPR55.
Authors: Hao Chang / Xiaoting Li / Ling Shen / Xuanrui Ge / Shuming Hao / Lijie Wu / Shenhui Liu / Junlin Liu / Vadim Cherezov / Tian Hua /
History
DepositionJul 30, 2024-
Header (metadata) releaseJan 1, 2025-
Map releaseJan 1, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60993.png

Downloads & links

-
Map

FileDownload / File: emd_60993.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å		0.83 Å/pix.
x 288 pix.
= 239.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.001793825 - 1.6755103
Average (Standard dev.)0.001111285 (±0.023839077)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 239.616 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60993_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60993_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody

EntireName: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
Components
  • Complex: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
    • Protein or peptide: G-protein coupled receptor 55,Soluble cytochrome b562
    • Protein or peptide: anti-BRIL Fab Heavy chain
    • Protein or peptide: anti-BRIL Fab Light chain
    • Protein or peptide: anti-Fab Nanobody
  • Ligand: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide

-
Supramolecule #1: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody

SupramoleculeName: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173 KDa

-
Macromolecule #1: G-protein coupled receptor 55,Soluble cytochrome b562

MacromoleculeName: G-protein coupled receptor 55,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.058051 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SGDCLFDGVN ELMKTLQFAV HIPTFVLGLL LNLLAIHVFS TFLKNRWPDY AATSIYMINL AVFDLLLVLS LPFKMVLSQV QSPFPSLCT LVECLYFVSM YGSVWTICFI SMDRFLAIRY PLLVSHLRSP RKAFGICCTI WVLVWTGSIP IYSFHGKVEK Y MCFHNMSD ...String:
SGDCLFDGVN ELMKTLQFAV HIPTFVLGLL LNLLAIHVFS TFLKNRWPDY AATSIYMINL AVFDLLLVLS LPFKMVLSQV QSPFPSLCT LVECLYFVSM YGSVWTICFI SMDRFLAIRY PLLVSHLRSP RKAFGICCTI WVLVWTGSIP IYSFHGKVEK Y MCFHNMSD DTWSAKVFFP LEVFGFLLPM GIMGFCCSRS IHILLGRRDH TQDWVQQKAC IYTIAASLAV FVVSFLPVHL GF FLQFLVR NSFIVECRAK QSISFFLQLS MCFSNVNCCL DVFIYYFVIK EFRMNIRAHR PSADLEDNWE TLNDNLKVIE KAD NAAQVK DALTKMRAAA LDAQKATPPK LEDKSPDSPE MKDFRHGFDI LVGQIDDALK LANEGKVKEA QAAAEQLKTT RNAY IQKYL ERARSTL

UniProtKB: G-protein coupled receptor 55, Soluble cytochrome b562

-
Macromolecule #2: anti-BRIL Fab Heavy chain

MacromoleculeName: anti-BRIL Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.152279 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSCIILFLVA TATGVHSEIS EVQLVESGGG LVQPGGSLRL SCAASGFNVR SFSIHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
WSCIILFLVA TATGVHSEIS EVQLVESGGG LVQPGGSLRL SCAASGFNVR SFSIHWVRQA PGKGLEWVAY ISSSSGSTSY ADSVKGRFT ISADTSKNTA YLQMNSLRAE DTAVYYCARW GYWPGEPWWK AFDYWGQGTL VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK KVEPKS

-
Macromolecule #3: anti-BRIL Fab Light chain

MacromoleculeName: anti-BRIL Fab Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.499129 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #4: anti-Fab Nanobody

MacromoleculeName: anti-Fab Nanobody / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.390644 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GSQVQLQESG GGLVQPGGSL RLSCAASGRT ISRYAMSWFR QAPGKEREFV AVARRSGDGA FYADSVQGRF TVSRDDAKNT VYLQMNSLK PEDTAVYYCA IDSDTFYSGS YDYWGQGTQV TVSS

-
Macromolecule #5: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-...

MacromoleculeName: 4-(3-bromanyl-5-ethoxy-4-oxidanyl-phenyl)-~{N}-(2-methoxyphenyl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxamide
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1L3E
Molecular weightTheoretical: 527.407 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ww2


Details: GPR55:AlphaFOLD2 other:6WW2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 452996
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Overall B value: 145.1
Output model

PDB-9iya:
Cryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex

+
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