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- PDB-8d1b: CryoEM structure of human orphan GPCR GPR179 in complex with extr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d1b | ||||||
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Title | CryoEM structure of human orphan GPCR GPR179 in complex with extracellular matrix protein pikachurin | ||||||
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![]() | SIGNALING PROTEIN / GPCR complex with ECM | ||||||
Function / homology | ![]() 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 / calcium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | ||||||
![]() | Patil, D.N. / Martemyanov, K.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 175.9 KB | Display | ![]() |
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PDB format | ![]() | 130.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 27121MC ![]() 7zc9C ![]() 7zcbC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 25642.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 81790.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: complex of GPR179 with pikachurin / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 217570 / Symmetry type: POINT | ||||||||||||||||||||||||
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