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- PDB-8d1b: CryoEM structure of human orphan GPCR GPR179 in complex with extr... -

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Basic information

Entry
Database: PDB / ID: 8d1b
TitleCryoEM structure of human orphan GPCR GPR179 in complex with extracellular matrix protein pikachurin
Components
  • Pikachurin
  • Probable G-protein coupled receptor 179
KeywordsSIGNALING PROTEIN / GPCR complex with ECM
Function / homology
Function and homology information


interstitial matrix / photoreceptor ribbon synapse / glycosaminoglycan binding / positive regulation of cell-substrate adhesion / presynaptic active zone / basement membrane / synaptic cleft / visual perception / extracellular matrix organization / cell projection ...interstitial matrix / photoreceptor ribbon synapse / glycosaminoglycan binding / positive regulation of cell-substrate adhesion / presynaptic active zone / basement membrane / synaptic cleft / visual perception / extracellular matrix organization / cell projection / G protein-coupled receptor activity / postsynaptic membrane / dendrite / calcium ion binding
Similarity search - Function
G-protein coupled receptor 158/179 / GPR158/179 extracellular domain / Laminin G domain / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal ...G-protein coupled receptor 158/179 / GPR158/179 extracellular domain / Laminin G domain / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Pikachurin / Probable G-protein coupled receptor 179
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsPatil, D.N. / Martemyanov, K.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH) United States
CitationJournal: Sci Signal / Year: 2023
Title: Structure of the photoreceptor synaptic assembly of the extracellular matrix protein pikachurin with the orphan receptor GPR179.
Authors: Dipak N Patil / Serena Pantalone / Yan Cao / Thibaut Laboute / Scott J Novick / Shikha Singh / Simone Savino / Silvia Faravelli / Francesca Magnani / Patrick R Griffin / Appu K Singh / ...Authors: Dipak N Patil / Serena Pantalone / Yan Cao / Thibaut Laboute / Scott J Novick / Shikha Singh / Simone Savino / Silvia Faravelli / Francesca Magnani / Patrick R Griffin / Appu K Singh / Federico Forneris / Kirill A Martemyanov /
Abstract: Precise synapse formation is essential for normal functioning of the nervous system. Retinal photoreceptors establish selective contacts with bipolar cells, aligning the neurotransmitter release ...Precise synapse formation is essential for normal functioning of the nervous system. Retinal photoreceptors establish selective contacts with bipolar cells, aligning the neurotransmitter release apparatus with postsynaptic signaling cascades. This involves transsynaptic assembly between the dystroglycan-dystrophin complex on the photoreceptor and the orphan receptor GPR179 on the bipolar cell, which is mediated by the extracellular matrix protein pikachurin (also known as EGFLAM). This complex plays a critical role in the synaptic organization of photoreceptors and signal transmission, and mutations affecting its components cause blinding disorders in humans. Here, we investigated the structural organization and molecular mechanisms by which pikachurin orchestrates transsynaptic assembly and solved structures of the human pikachurin domains by x-ray crystallography and of the GPR179-pikachurin complex by single-particle, cryo-electron microscopy. The structures reveal molecular recognition principles of pikachurin by the Cache domains of GPR179 and show how the interaction is involved in the transsynaptic alignment of the signaling machinery. Together, these data provide a structural basis for understanding the synaptic organization of photoreceptors and ocular pathology.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 9, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)214,8654
Polymers214,8654
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Pikachurin / Agrin-like protein / EGF-like / fibronectin type-III and laminin G-like domain-containing protein


Mass: 25642.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFLAM, AGRINL, AGRNL, PIKA / Production host: Homo sapiens (human) / References: UniProt: Q63HQ2
#2: Protein Probable G-protein coupled receptor 179 / Probable G-protein coupled receptor 158-like 1 / GPR158-like


Mass: 81790.227 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: Homo sapiens (human) / 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: complex of GPR179 with pikachurin / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217570 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066858
ELECTRON MICROSCOPYf_angle_d0.9859294
ELECTRON MICROSCOPYf_dihedral_angle_d19.869958
ELECTRON MICROSCOPYf_chiral_restr0.0521010
ELECTRON MICROSCOPYf_plane_restr0.0081232

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