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- PDB-9fte: Cryo-EM structure of the adhesion GPCR ADGRV1 in complex with a n... -

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Basic information

Entry
Database: PDB / ID: 9fte
TitleCryo-EM structure of the adhesion GPCR ADGRV1 in complex with a nanobody
Components
  • Adhesion G protein-coupled receptor V1
  • Nanobody RE02
KeywordsMEMBRANE PROTEIN / Adhesion GPCR / Signaling / 7TM / Nanobody
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.82 Å
AuthorsAchat, Y. / Prevost, M. / Mechaly, A. / Genera, M. / Colcombet, J.B. / Bezault, A. / Winter, J.M. / Ayme, G. / Venien-Bryan, C. / Wolff, N.
Funding support France, 2items
OrganizationGrant numberCountry
Other government2019-0018C1 Fondation pour l'Audition France
Other government4133/2021 Ministere de l'enseignement superieur et de la recherche France
Citation
Journal: To Be Published
Title: Cryo-EM structure of the adhesion GPCR ADGRV1 in complex with a nanobody
Authors: Achat, Y. / Prevost, M. / Mechaly, A. / Genera, M. / Colcombet, J.B. / Bezault, A. / Winter, J.M. / Ayme, G. / Venien-Bryan, C. / Wolff, N.
#1: Journal: 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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesion G protein-coupled receptor V1
B: Nanobody RE02


Theoretical massNumber of molelcules
Total (without water)63,1002
Polymers63,1002
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Adhesion G protein-coupled receptor V1


Mass: 47335.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1- / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adgrv1, Gpr98 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B8JJE0
#2: Antibody Nanobody RE02


Mass: 15764.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 128-137 : c-Myc tag 142-147 : 6x His tag / Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
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

Component
IDNameTypeEntity IDParent-IDSource
1Adhesion G-protein coupled receptor V1 beta subunit complexed with RE02 nanobodyCOMPLEXall0MULTIPLE SOURCES
2RE02 nanobodyCOMPLEX#21RECOMBINANT
3Adhesion G-protein coupled receptor V1 beta subunitCOMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Vicugna pacos (alpaca)30538
43Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
32Escherichia coli (E. coli)562
43Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
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: 2600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97447 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042869
ELECTRON MICROSCOPYf_angle_d0.7083913
ELECTRON MICROSCOPYf_dihedral_angle_d4.707393
ELECTRON MICROSCOPYf_chiral_restr0.041434
ELECTRON MICROSCOPYf_plane_restr0.007486

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