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- EMDB-27121: CryoEM structure of human orphan GPCR GPR179 in complex with extr... -

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Basic information

Entry
Database: EMDB / ID: EMD-27121
TitleCryoEM structure of human orphan GPCR GPR179 in complex with extracellular matrix protein pikachurin
Map dataStructure of an orphan GPCR complexed with ECM protein
Sample
  • Complex: complex of GPR179 with pikachurin
    • Protein or peptide: Probable G-protein coupled receptor 179
    • Protein or peptide: Pikachurin
KeywordsGPCR complex with ECM / SIGNALING PROTEIN
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. / EGF-like domain signature 1. / Fibronectin type III domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 Å
AuthorsPatil DN / Martemyanov KA
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27121.png

Downloads & links

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Map

FileDownload / File: emd_27121.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of an orphan GPCR complexed with ECM protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å		0.86 Å/pix.
x 480 pix.
= 410.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.54
Minimum - Maximum-1.8207523 - 3.3516273
Average (Standard dev.)-0.0014532256 (±0.04054495)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 410.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27121_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27121_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : complex of GPR179 with pikachurin

EntireName: complex of GPR179 with pikachurin
Components
  • Complex: complex of GPR179 with pikachurin
    • Protein or peptide: Probable G-protein coupled receptor 179
    • Protein or peptide: Pikachurin

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Supramolecule #1: complex of GPR179 with pikachurin

SupramoleculeName: complex of GPR179 with pikachurin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Pikachurin

MacromoleculeName: Pikachurin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.64225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AAHPCVRAPC AHGGSCRPRK EGYDCDCPLG FEGLHCQKEC GNYCLNTIIE AIEIPQFIGR SYLTYDNPDI LKRVSGSRSN VFMRFKTTA KDGLLLWRGD SPMRPNSDFI SLGLRDGALV FSYNLGSGVA SIMVNGSFND GRWHRVKAVR DGQSGKITVD D YGARTGKS ...String:
AAHPCVRAPC AHGGSCRPRK EGYDCDCPLG FEGLHCQKEC GNYCLNTIIE AIEIPQFIGR SYLTYDNPDI LKRVSGSRSN VFMRFKTTA KDGLLLWRGD SPMRPNSDFI SLGLRDGALV FSYNLGSGVA SIMVNGSFND GRWHRVKAVR DGQSGKITVD D YGARTGKS PGMMRQLNIN GALYVGGMKE IALHTNRQYM RGLVGCISHF TLSTDYHISL VEDAVDGKNI NTCGAC

UniProtKB: Pikachurin

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Macromolecule #2: Probable G-protein coupled receptor 179

MacromoleculeName: Probable G-protein coupled receptor 179 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.790227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGTRGAVMPP PMWGLLGCCF VCAWALGGPR PIRSLPPLSS QVKPGSVPMQ VPLEGAEAAL AYLYSGDAQQ LSQVNCSERY EARGAGAMP GLPPSLQGAA GTLAQAANFL NMLLQANDIR ESSVEEDVEW YQALVRSVAE GDPRVYRALL TFNPPPGASH L QLALQATR ...String:
MGTRGAVMPP PMWGLLGCCF VCAWALGGPR PIRSLPPLSS QVKPGSVPMQ VPLEGAEAAL AYLYSGDAQQ LSQVNCSERY EARGAGAMP GLPPSLQGAA GTLAQAANFL NMLLQANDIR ESSVEEDVEW YQALVRSVAE GDPRVYRALL TFNPPPGASH L QLALQATR TGEETILQDL SGNWVQEENP PGDLDTPALK KRVLTNDLGS LGSPKWPQAD GYVGDTQQVR LSPPFLECQE GR LRPGWLI TLSATFYGLK PDLSPEVRGQ VQMDVDLQSV DINQCASGPG WYSNTHLCDL NSTQCVPLES QGFVLGRYLC RCR PGFYGA SPSGGLEESD FQTTGQFGFP EGRSGRLLQC LPCPEGCTSC MDATPCLVEE AAVLRAAVLA CQACCMLAIF LSML VSYRC RRNKRIWASG VVLLETVLFG FLLLYFPVFI LYFKPSVFRC IALRWVRLLG FAIVYGTIIL KLYRVLQLFL SRTAQ RSAL LSSGRLLRRL GLLLLPVLGF LAVWTVGALE RGIQHAPLVI RGHTPSGRHF YLCHHDRWDY IMVVAELLLL CWGSFL CYA TRAVLSAFHE PRYMGIALHN ELLLSAAFHT ARFVLVPSLH PDWTLLLFFF HTHSTVTTTL ALIFIPKFWK LGAPPRE EM VDEVCEDELD LQHSGSYLGS SIASAWSEHS LDPGDIRDEL KKLYAQLEVH KTKEMAANNP HLPKKRGSSC QGLGRSFM R YLAEFPEALA RQHSRDSGS

UniProtKB: Probable G-protein coupled receptor 179

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: alphafold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 217570
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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