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- EMDB-35497: Complex structure of Neuropeptide Y Y2 receptor in complex with P... -

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Basic information

Entry
Database: EMDB / ID: EMD-35497
TitleComplex structure of Neuropeptide Y Y2 receptor in complex with PYY(3-36) and Gi (Consensus map)
Map dataConsensus map (PYY(3-36)-Y2R-Gi-scFv16)
Sample
  • Complex: Complex structure of PYY(3-36)-Y2R-Gi-scFv16
    • Complex: Guanine nucleotide-binding protein
    • Complex: scFv16
    • Complex: PYY(3-36)
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsKang H / Park C / Kim J / Choi H-J
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063903 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2020R1A2C2003783 Korea, Republic Of
CitationJournal: Structure / Year: 2023
Title: Structural basis for Y2 receptor-mediated neuropeptide Y and peptide YY signaling.
Authors: Hyunook Kang / Chaehee Park / Yeol Kyo Choi / Jungnam Bae / Sohee Kwon / Jinuk Kim / Chulwon Choi / Chaok Seok / Wonpil Im / Hee-Jung Choi /
Abstract: Neuropeptide Y (NPY) and its receptors are expressed in various human tissues including the brain where they regulate appetite and emotion. Upon NPY stimulation, the neuropeptide Y1 and Y2 receptors ...Neuropeptide Y (NPY) and its receptors are expressed in various human tissues including the brain where they regulate appetite and emotion. Upon NPY stimulation, the neuropeptide Y1 and Y2 receptors (YR and YR, respectively) activate G signaling, but their physiological responses to food intake are different. In addition, deletion of the two N-terminal amino acids of peptide YY (PYY(3-36)), the endogenous form found in circulation, can stimulate YR but not YR, suggesting that YR and YR may have distinct ligand-binding modes. Here, we report the cryo-electron microscopy structures of the PYY(3-36)‒YR‒G and NPY‒YR‒G complexes. Using cell-based assays, molecular dynamics simulations, and structural analysis, we revealed the molecular basis of the exclusive binding of PYY(3-36) to YR. Furthermore, we demonstrated that YR favors G protein signaling over β-arrestin signaling upon activation, whereas YR does not show a preference between these two pathways.
History
DepositionFeb 28, 2023-
Header (metadata) releaseMar 22, 2023-
Map releaseMar 22, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35497.png

Downloads & links

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Map

FileDownload / File: emd_35497.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map (PYY(3-36)-Y2R-Gi-scFv16)
Voxel sizeX=Y=Z: 0.849 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.6419808 - 2.3113759
Average (Standard dev.)-0.00019970682 (±0.029740492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 339.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_35497_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_35497_half_map_2.map
AnnotationHalf map B
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 structure of PYY(3-36)-Y2R-Gi-scFv16

EntireName: Complex structure of PYY(3-36)-Y2R-Gi-scFv16
Components
  • Complex: Complex structure of PYY(3-36)-Y2R-Gi-scFv16
    • Complex: Guanine nucleotide-binding protein
    • Complex: scFv16
    • Complex: PYY(3-36)

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Supramolecule #1: Complex structure of PYY(3-36)-Y2R-Gi-scFv16

SupramoleculeName: Complex structure of PYY(3-36)-Y2R-Gi-scFv16 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Guanine nucleotide-binding protein

SupramoleculeName: Guanine nucleotide-binding protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3, #5

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Supramolecule #3: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: PYY(3-36)

SupramoleculeName: PYY(3-36) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4

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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

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 12262301
Startup modelType of model: OTHER
Details: Initial 3D volume generated by ab initio reconstruction
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 359459
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7ddz

chain_id: A

7vgx

chain_id: A

7vgx

chain_id: B

7vgx

chain_id: G

7vgx

chain_id: S
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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