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- PDB-8irj: Cryo-EM structure of an orphan GPCR -

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Basic information

Entry
Database: PDB / ID: 8irj
TitleCryo-EM structure of an orphan GPCR
ComponentsProbable G-protein coupled receptor 179
KeywordsSIGNALING PROTEIN / GPCR
Function / homology
Function and homology information


visual perception / G protein-coupled receptor activity / postsynaptic membrane / dendrite
Similarity search - Function
G-protein coupled receptor 158/179 / : / GPR158/179 extracellular domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
Probable G-protein coupled receptor 179
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsYun, Y. / Jeong, H. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To be published
Title: Cryo-EM structure of an orphan GPCR
Authors: Yun, Y. / Jeong, H. / Lee, H.H.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable G-protein coupled receptor 179
B: Probable G-protein coupled receptor 179


Theoretical massNumber of molelcules
Total (without water)167,9182
Polymers167,9182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Probable G-protein coupled receptor 179 / Probable G-protein coupled receptor 158-like 1 / GPR158-like


Mass: 83958.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPR179, GPR158L, GPR158L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PRD1
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: Orphan GPCR / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2250 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 1.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 668157 / Symmetry type: POINT
RefinementHighest resolution: 3.49 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068378
ELECTRON MICROSCOPYf_angle_d1.09311386
ELECTRON MICROSCOPYf_dihedral_angle_d6.361142
ELECTRON MICROSCOPYf_chiral_restr0.0771300
ELECTRON MICROSCOPYf_plane_restr0.0091442

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