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- EMDB-50743: Cryo-EM structure of the adhesion GPCR ADGRV1 in complex with a n... -

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Basic information

Entry
Database: EMDB / ID: EMD-50743
TitleCryo-EM structure of the adhesion GPCR ADGRV1 in complex with a nanobody
Map dataEM map
Sample
  • Complex: Adhesion G-protein coupled receptor V1 beta subunit complexed with RE02 nanobody
    • Complex: RE02 nanobody
      • Protein or peptide: Nanobody RE02
    • Complex: Adhesion G-protein coupled receptor V1 beta subunit
      • Protein or peptide: Adhesion G protein-coupled receptor V1
KeywordsAdhesion GPCR / Signaling / 7TM / Nanobody / MEMBRANE PROTEIN
Function / homology
Function and homology information


maintenance of animal organ identity / stereocilium membrane / sensory perception of light stimulus / photoreceptor cell maintenance / neurogenesis / photoreceptor inner segment / sensory perception of sound / G protein-coupled receptor activity / cell surface receptor signaling pathway / receptor complex ...maintenance of animal organ identity / stereocilium membrane / sensory perception of light stimulus / photoreceptor cell maintenance / neurogenesis / photoreceptor inner segment / sensory perception of sound / G protein-coupled receptor activity / cell surface receptor signaling pathway / receptor complex / hydrolase activity / calcium ion binding / cell surface / cytoplasm
Similarity search - Function
Adhesion G-protein coupled receptor V1 / Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Domains in Na-Ca exchangers and integrin-beta4 / Na-Ca exchanger/integrin-beta4 / Calx-beta domain ...Adhesion G-protein coupled receptor V1 / Leucine-rich glioma-inactivated , EPTP repeat / EAR / EPTP domain / EAR repeat profile. / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Domains in Na-Ca exchangers and integrin-beta4 / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / CalX-like domain superfamily / Concanavalin A-like lectin/glucanases superfamily / GAIN domain superfamily / : / GAIN-B domain profile. / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Adhesion G-protein coupled receptor V1
Similarity search - Component
Biological speciesMus musculus (house mouse) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsAchat Y / Prevost M / Mechaly A / Genera M / Colcombet JB / Bezault A / Winter JM / Ayme G / Venien-Bryan C / Wolff N
Funding support France, 2 items
OrganizationGrant numberCountry
Other government2019-0018C1 Fondation pour l'Audition France
Other government4133/2021 Ministere de l'enseignement superieur et de la recherche France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionJun 24, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50743.png

Downloads & links

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Map

FileDownload / File: emd_50743.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 308. Å		1.03 Å/pix.
x 300 pix.
= 308. Å		1.03 Å/pix.
x 300 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.6298756 - 0.74843574
Average (Standard dev.)-0.00042834 (±0.010410258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: A

Fileemd_50743_half_map_1.map
AnnotationA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B

Fileemd_50743_half_map_2.map
AnnotationB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adhesion G-protein coupled receptor V1 beta subunit complexed wit...

EntireName: Adhesion G-protein coupled receptor V1 beta subunit complexed with RE02 nanobody
Components
  • Complex: Adhesion G-protein coupled receptor V1 beta subunit complexed with RE02 nanobody
    • Complex: RE02 nanobody
      • Protein or peptide: Nanobody RE02
    • Complex: Adhesion G-protein coupled receptor V1 beta subunit
      • Protein or peptide: Adhesion G protein-coupled receptor V1

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Supramolecule #1: Adhesion G-protein coupled receptor V1 beta subunit complexed wit...

SupramoleculeName: Adhesion G-protein coupled receptor V1 beta subunit complexed with RE02 nanobody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: RE02 nanobody

SupramoleculeName: RE02 nanobody / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: Adhesion G-protein coupled receptor V1 beta subunit

SupramoleculeName: Adhesion G-protein coupled receptor V1 beta subunit / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Adhesion G protein-coupled receptor V1

MacromoleculeName: Adhesion G protein-coupled receptor V1 / type: protein_or_peptide / ID: 1 / Details: 1- / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 47.335199 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SVYAVYAQTD NSSSYNEAFF SAGLICISGL CLAVVSHMFC ARHSMFAAKL LTHMMVASLG TQILFLASAY ASPHLSEESC SAVAAVAHY LYLCQFSWML IQSVNFWYVL VVSDEHTERR CLLFCLLSWG LPSFVVILLI LILRGIYHRS MPQIYGLIHG D LCFIPNIY ...String:
SVYAVYAQTD NSSSYNEAFF SAGLICISGL CLAVVSHMFC ARHSMFAAKL LTHMMVASLG TQILFLASAY ASPHLSEESC SAVAAVAHY LYLCQFSWML IQSVNFWYVL VVSDEHTERR CLLFCLLSWG LPSFVVILLI LILRGIYHRS MPQIYGLIHG D LCFIPNIY AALFTAALVP LMCLVVVFVV FIHAYQLKPQ WKGYDDVFRG RTNAAEIPLI LYLFALISMT WLWGGLHMAY RH FWMLVLF VIFNSLQGLY VFVVYFILHN QTCCPMKASY TVEMNGHPGP STAFFTPGSG IPPAGEINKS TQNLINAMEE VPS DWERSS FQQTSQASPD LKTSPQNGAS FPSSGGYGPG SLIADEESQE FDDLIFALKT GAGLSVSDNE SGQGSQEGGT LTDS QIVEL RRIPIADTHL SGRHHHHHHH H

UniProtKB: Adhesion G-protein coupled receptor V1

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Macromolecule #2: Nanobody RE02

MacromoleculeName: Nanobody RE02 / type: protein_or_peptide / ID: 2 / Details: 128-137 : c-Myc tag 142-147 : 6x His tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 15.764383 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAEVQLVESG GGLVQPGGSL RLSCAASGSS FSINAMGWYR QAPGKQRELV AAISRGGSTN YASSVKGRFT ISRDNGKNTV YLQMNSPKP EDTAVYYCNV GSRSTLPIWY DYWGQGTQVT VSSAAAEQKL ISEEDLNGAA HHHHHHGS

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 97447
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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