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

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Basic information

Entry
Database: PDB / ID: 9iya
TitleCryo-EM structure of GPR55-Fab-Nb-ONO-9710531 complex
Components
  • G-protein coupled receptor 55,Soluble cytochrome b562
  • anti-BRIL Fab Heavy chain
  • anti-BRIL Fab Light chain
  • anti-Fab Nanobody
KeywordsSTRUCTURAL PROTEIN / GPCR / G protein / cryo-EM / membrane 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsHua, T. / Liu, Z.J. / Cherezov, V. / Chang, H. / Li, X.T. / Shen, L.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein coupled receptor 55,Soluble cytochrome b562
H: anti-BRIL Fab Heavy chain
L: anti-BRIL Fab Light chain
N: anti-Fab Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6285
Polymers110,1004
Non-polymers5271
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein G-protein coupled receptor 55,Soluble cytochrome b562 / Cytochrome b-562


Mass: 47058.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR55, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y2T6, UniProt: P0ABE7
#2: Antibody anti-BRIL Fab Heavy chain


Mass: 26152.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody anti-BRIL Fab Light chain


Mass: 23499.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#4: Antibody anti-Fab Nanobody


Mass: 13390.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Chemical ChemComp-A1L3E / 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


Mass: 527.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27BrN2O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of GPR55 with anti-BRIL Fab and anti-Fab Nanobody
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.173 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 452996 / Symmetry type: POINT
Atomic model buildingB value: 145.1 / Protocol: RIGID BODY FIT

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