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- EMDB-33069: Cryo-EM structure of neuropeptide Y Y1 receptor in complex with N... -

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Basic information

Entry
Database: EMDB / ID: EMD-33069
TitleCryo-EM structure of neuropeptide Y Y1 receptor in complex with NPY and Gi
Map data
Sample
  • Complex: Neuropeptide Y Y1 receptor in complex with NPY and Gi
    • Complex: Neuropeptide Y Y1 receptor and Gi
      • Protein or peptide: Neuropeptide Y receptor type 1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Neuropeptide Y
      • Protein or peptide: Neuropeptide Y
Function / homology
Function and homology information


pancreatic polypeptide receptor activity / regulation of nerve growth factor production / peptide YY receptor activity / short-day photoperiodism / neuropeptide activity / negative regulation of acute inflammatory response to antigenic stimulus / neuropeptide Y receptor activity / monocyte activation / positive regulation of dopamine metabolic process / neuropeptide Y receptor binding ...pancreatic polypeptide receptor activity / regulation of nerve growth factor production / peptide YY receptor activity / short-day photoperiodism / neuropeptide activity / negative regulation of acute inflammatory response to antigenic stimulus / neuropeptide Y receptor activity / monocyte activation / positive regulation of dopamine metabolic process / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / positive regulation of appetite / synaptic signaling via neuropeptide / positive regulation of eating behavior / adult feeding behavior / neuropeptide receptor activity / regulation of presynaptic cytosolic calcium ion concentration / drinking behavior / neuropeptide hormone activity / positive regulation of cell-substrate adhesion / feeding behavior / regulation of nitric oxide biosynthetic process / neuropeptide binding / regulation of synaptic vesicle exocytosis / central nervous system neuron development / regulation of multicellular organism growth / outflow tract morphogenesis / developmental growth / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuronal dense core vesicle / negative regulation of blood pressure / regulation of eating behavior / adenylate cyclase inhibitor activity / T cell migration / positive regulation of protein localization to cell cortex / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / sensory perception of pain / D2 dopamine receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / cellular response to forskolin / Peptide ligand-binding receptors / regulation of mitotic spindle organization / locomotory behavior / mast cell degranulation / chemokine-mediated signaling pathway / calcium channel regulator activity / neuropeptide signaling pathway / Regulation of insulin secretion / response to prostaglandin E / cerebral cortex development / positive regulation of cholesterol biosynthetic process / glucose metabolic process / regulation of blood pressure / G protein-coupled receptor binding / response to peptide hormone / GABA-ergic synapse / G protein-coupled receptor activity / neuron projection development / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / terminal bouton / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / Prostacyclin signalling through prostacyclin receptor / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / GDP binding / G beta:gamma signalling through BTK / photoreceptor disc membrane / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to prostaglandin E stimulus / GPER1 signaling / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / G alpha (12/13) signalling events / extracellular vesicle
Similarity search - Function
Neuropeptide Y1 receptor / Neuropeptide Y receptor family / Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion ...Neuropeptide Y1 receptor / Neuropeptide Y receptor family / Pancreatic hormone-like / Pancreatic hormone-like, conserved site / Pancreatic hormone peptide / Pancreatic hormone family signature. / Pancreatic hormone family profile. / Pancreatic hormones / neuropeptide F / peptide YY family / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Pro-neuropeptide Y / Neuropeptide Y receptor type 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsTang T / Han S / Zhao Q / Wu B
Funding support China, 3 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31825010 China
National Science Foundation (NSF, China)82121005 China
National Science Foundation (NSF, China)32161133011 China
CitationJournal: Sci Adv / Year: 2022
Title: Receptor-specific recognition of NPY peptides revealed by structures of NPY receptors.
Authors: Tingting Tang / Qiuxiang Tan / Shuo Han / Anne Diemar / Kristin Löbner / Hongyu Wang / Corinna Schüß / Victoria Behr / Karin Mörl / Mu Wang / Xiaojing Chu / Cuiying Yi / Max Keller / ...Authors: Tingting Tang / Qiuxiang Tan / Shuo Han / Anne Diemar / Kristin Löbner / Hongyu Wang / Corinna Schüß / Victoria Behr / Karin Mörl / Mu Wang / Xiaojing Chu / Cuiying Yi / Max Keller / Jacob Kofoed / Steffen Reedtz-Runge / Anette Kaiser / Annette G Beck-Sickinger / Qiang Zhao / Beili Wu /
Abstract: In response to three highly conserved neuropeptides, neuropeptide Y (NPY), peptide YY, and pancreatic polypeptide (PP), four G protein-coupled receptors mediate multiple essential physiological ...In response to three highly conserved neuropeptides, neuropeptide Y (NPY), peptide YY, and pancreatic polypeptide (PP), four G protein-coupled receptors mediate multiple essential physiological processes, such as food intake, vasoconstriction, sedation, and memory retention. Here, we report the structures of the human Y, Y, and Y receptors in complex with NPY or PP, and the G protein. These structures reveal distinct binding poses of the peptide upon coupling to different receptors, reflecting the importance of the conformational plasticity of the peptide in recognizing the NPY receptors. The N terminus of the peptide forms extensive interactions with the Y receptor, but not with the Y and Y receptors. Supported by mutagenesis and functional studies, subtype-specific interactions between the receptors and peptides were further observed. These findings provide insight into key factors that govern NPY signal recognition and transduction, and would enable development of selective drugs.
History
DepositionMar 15, 2022-
Header (metadata) releaseMay 18, 2022-
Map releaseMay 18, 2022-
UpdateMay 18, 2022-
Current statusMay 18, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33069.png

Downloads & links

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Map

FileDownload / File: emd_33069.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 Å		1.05 Å/pix.
x 256 pix.
= 267.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.296
Minimum - Maximum-0.9158801 - 1.7866732
Average (Standard dev.)0.00027756614 (±0.04489177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Neuropeptide Y Y1 receptor in complex with NPY and Gi

EntireName: Neuropeptide Y Y1 receptor in complex with NPY and Gi
Components
  • Complex: Neuropeptide Y Y1 receptor in complex with NPY and Gi
    • Complex: Neuropeptide Y Y1 receptor and Gi
      • Protein or peptide: Neuropeptide Y receptor type 1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Neuropeptide Y
      • Protein or peptide: Neuropeptide Y

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Supramolecule #1: Neuropeptide Y Y1 receptor in complex with NPY and Gi

SupramoleculeName: Neuropeptide Y Y1 receptor in complex with NPY and Gi / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Neuropeptide Y Y1 receptor and Gi

SupramoleculeName: Neuropeptide Y Y1 receptor and Gi / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4

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Supramolecule #3: Neuropeptide Y

SupramoleculeName: Neuropeptide Y / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5

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Macromolecule #1: Neuropeptide Y receptor type 1

MacromoleculeName: Neuropeptide Y receptor type 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.462648 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSTLFSQVE NHSVHSNFSE KNAQLLAFEN DDCHLPLAMI FTLALAYGAV IILGVSGNLA LIIIILKQKE MRNVTNILIV NLSFSDLLV AIMCLPFTFV YTLMDHWVFG EAMCKLNPFV QCVSITVSIF SLVLIAVERH QLIINPRGWR PNNRHAYVGI A VIWVLAVA ...String:
MNSTLFSQVE NHSVHSNFSE KNAQLLAFEN DDCHLPLAMI FTLALAYGAV IILGVSGNLA LIIIILKQKE MRNVTNILIV NLSFSDLLV AIMCLPFTFV YTLMDHWVFG EAMCKLNPFV QCVSITVSIF SLVLIAVERH QLIINPRGWR PNNRHAYVGI A VIWVLAVA SSLPFLIYQV MTDEPFQNVT LDAYKDKYVC FDQFPSDSHR LSYTTLLLVL QYFGPLCFIF ICYFKIYIRL KR RNNMMDK MRDNKYRSSE TKRINIMLLS IVVAFAVCWL PLTIFNTVFD WNHQIIATCN HNLLFLLCHL TAMISTCVNP IFY GFLNKN FQRDLQFFFN FCDFEFLEVL FQGPWSHPQF EKGGGSGGGS GGSAWSHPQF EK

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Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.414047 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHASM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.744371 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String:
MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWN

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #5: Neuropeptide Y

MacromoleculeName: Neuropeptide Y / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.277735 KDa
SequenceString:
YPSKPDNPGE DAPAEDMARY YSALRHYINL ITRQR(TYC)

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 423400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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