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- EMDB-31979: Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31979
TitleNeuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and its endogeneous Peptide-Agonist Neuropeptide Y (NPY)
Map dataMerged density of NPY-Y1R-Gi-scFv16 complex generated by vop maximum
Sample
  • Complex: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneous Peptide-Agonist Neuropeptide Y (NPY), G Protein and G-protein stabilizing antibody fragement (scFv16)
    • Complex: Neuropeptide Y Y1 Receptor (NPY1R)
      • Protein or peptide: Neuropeptide Y receptor type 1
    • Complex: nucleotide-free G-Protein heterotrimer
      • 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
    • Complex: single-chain antibody Fv fragment (scFv16)
      • Protein or peptide: single-chain antibody Fv fragment (scFv16)
Function / homology
Function and homology information


pancreatic polypeptide receptor activity / regulation of nerve growth factor production / peptide YY receptor activity / short-day photoperiodism / negative regulation of acute inflammatory response to antigenic stimulus / neuropeptide Y receptor activity / monocyte activation / positive regulation of dopamine metabolic process / positive regulation of nitric oxide metabolic process / positive regulation of appetite ...pancreatic polypeptide receptor activity / regulation of nerve growth factor production / peptide YY receptor activity / short-day photoperiodism / negative regulation of acute inflammatory response to antigenic stimulus / neuropeptide Y receptor activity / monocyte activation / positive regulation of dopamine metabolic process / positive regulation of nitric oxide metabolic process / positive regulation of appetite / neuropeptide Y receptor binding / intestinal epithelial cell differentiation / synaptic signaling via neuropeptide / positive regulation of eating behavior / adult feeding behavior / neuropeptide receptor activity / regulation of presynaptic cytosolic calcium ion concentration / neuropeptide hormone activity / neuropeptide binding / feeding behavior / positive regulation of cell-substrate adhesion / neuronal dense core vesicle / regulation of synaptic vesicle exocytosis / central nervous system neuron development / outflow tract morphogenesis / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / regulation of multicellular organism growth / neuropeptide signaling pathway / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / negative regulation of blood pressure / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / adenylate cyclase-inhibiting serotonin receptor signaling pathway / sensory perception of pain / cellular response to forskolin / regulation of mitotic spindle organization / Peptide ligand-binding receptors / calcium channel regulator activity / Regulation of insulin secretion / locomotory behavior / positive regulation of cholesterol biosynthetic process / G protein-coupled receptor binding / negative regulation of insulin secretion / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cerebral cortex development / GABA-ergic synapse / response to peptide hormone / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / regulation of blood pressure / centriolar satellite / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / glucose metabolic process / terminal bouton / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / neuron projection development / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / GDP binding / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs)
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 / Guanine nucleotide binding protein (G-protein), alpha subunit ...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 / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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(O) subunit gamma-2 / 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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPark C / Kim J / Jeong H / Kang H / Bang I / 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)2020R1A2C2003783 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis of neuropeptide Y signaling through Y1 receptor.
Authors: Chaehee Park / Jinuk Kim / Seung-Bum Ko / Yeol Kyo Choi / Hyeongseop Jeong / Hyeonuk Woo / Hyunook Kang / Injin Bang / Sang Ah Kim / Tae-Young Yoon / Chaok Seok / Wonpil Im / Hee-Jung Choi /
Abstract: Neuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, ...Neuropeptide Y (NPY) is highly abundant in the brain and involved in various physiological processes related to food intake and anxiety, as well as human diseases such as obesity and cancer. However, the molecular details of the interactions between NPY and its receptors are poorly understood. Here, we report a cryo-electron microscopy structure of the NPY-bound neuropeptide Y1 receptor (YR) in complex with G protein. The NPY C-terminal segment forming the extended conformation binds deep into the YR transmembrane core, where the amidated C-terminal residue Y36 of NPY is located at the base of the ligand-binding pocket. Furthermore, the helical region and two N-terminal residues of NPY interact with YR extracellular loops, contributing to the high affinity of NPY for YR. The structural analysis of NPY-bound YR and mutagenesis studies provide molecular insights into the activation mechanism of YR upon NPY binding.
History
DepositionSep 19, 2021-
Header (metadata) releaseFeb 23, 2022-
Map releaseFeb 23, 2022-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
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  • Surface view colored by height
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  • Atomic models: PDB-7vgx
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31979.png

Downloads & links

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Map

FileDownload / File: emd_31979.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMerged density of NPY-Y1R-Gi-scFv16 complex generated by vop maximum
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 346. Å		0.87 Å/pix.
x 400 pix.
= 346. Å		0.87 Å/pix.
x 400 pix.
= 346. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.865 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-1.4886115 - 9.971682
Average (Standard dev.)0.03531131 (±0.13182767)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 346.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8650.8650.865
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z346.000346.000346.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-1.4899.9720.035

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Supplemental data

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Additional map: Local refined density of NPY-Y1R complex

Fileemd_31979_additional_1.map
AnnotationLocal refined density of NPY-Y1R complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refined density of Gi-scFv16 complex

Fileemd_31979_additional_2.map
AnnotationLocal refined density of Gi-scFv16 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density of NPY-Y1R-Gi-scFv16 complex generated by non-uniform refinement...

Fileemd_31979_additional_3.map
AnnotationDensity of NPY-Y1R-Gi-scFv16 complex generated by non-uniform refinement
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 Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneou...

EntireName: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneous Peptide-Agonist Neuropeptide Y (NPY), G Protein and G-protein stabilizing antibody fragement (scFv16)
Components
  • Complex: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneous Peptide-Agonist Neuropeptide Y (NPY), G Protein and G-protein stabilizing antibody fragement (scFv16)
    • Complex: Neuropeptide Y Y1 Receptor (NPY1R)
      • Protein or peptide: Neuropeptide Y receptor type 1
    • Complex: nucleotide-free G-Protein heterotrimer
      • 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
    • Complex: single-chain antibody Fv fragment (scFv16)
      • Protein or peptide: single-chain antibody Fv fragment (scFv16)

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Supramolecule #1: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneou...

SupramoleculeName: Complex of Neuropeptide Y Y1 Receptor (NPY1R) with its endogeneous Peptide-Agonist Neuropeptide Y (NPY), G Protein and G-protein stabilizing antibody fragement (scFv16)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 160 KDa

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Supramolecule #2: Neuropeptide Y Y1 Receptor (NPY1R)

SupramoleculeName: Neuropeptide Y Y1 Receptor (NPY1R) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: nucleotide-free G-Protein heterotrimer

SupramoleculeName: nucleotide-free G-Protein heterotrimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Neuropeptide Y

SupramoleculeName: Neuropeptide Y / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2

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Supramolecule #5: single-chain antibody Fv fragment (scFv16)

SupramoleculeName: single-chain antibody Fv fragment (scFv16) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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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: 46.489961 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DYKDDDDAID MNSTLFSQVE NHSVHSNFSE KNAQLLAFEN DDCHLPLAMI FTLALAYGAV IILGVSGNLA LIIIILKQKE MRNVTNILI VNLSFSDLLV AIMCLPFTFV YTLMDHWVFG EAMCKLNPFV QCVSITVSIF SLVLIAVERH QLIINPRGWR P NNRHAYVG ...String:
DYKDDDDAID MNSTLFSQVE NHSVHSNFSE KNAQLLAFEN DDCHLPLAMI FTLALAYGAV IILGVSGNLA LIIIILKQKE MRNVTNILI VNLSFSDLLV AIMCLPFTFV YTLMDHWVFG EAMCKLNPFV QCVSITVSIF SLVLIAVERH QLIINPRGWR P NNRHAYVG IAVIWVLAVA SSLPFLIYQV MTDEPFQNVT LDAYKDKYVC FDQFPSDSHR LSYTTLLLVL QYFGPLCFIF IC YFKIYIR LKRRNNMMDK MRDNKYRSSE TKRINIMLLS IVVAFAVCWL PLTIFNTVFD WNHQIIATCN HNLLFLLCHL TAM ISTCVN PIFYGFLNKN FQRDLQFFFN FCDFRSRDDD YETIAMSTMH TDVSKTSLKQ ASPVAFKKIN NNDDNEKIAS LEVL FQ

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Macromolecule #2: Neuropeptide Y

MacromoleculeName: Neuropeptide Y / type: protein_or_peptide / ID: 2 / 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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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.427969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSGCTLSAED KAAVERSKMI DRNLREDGEK AAREVKLLLL GAGESGKSTI VKQMKIIHEA GYSEEECKQY KAVVYSNTIQ SIIAIIRAM GRLKIDFGDS ARADDARQLF VLAGAAEEGF MTAELAGVIK RLWKDSGVQA CFNRSREYQL NDSAAYYLND L DRIAQPNY ...String:
GSGCTLSAED KAAVERSKMI DRNLREDGEK AAREVKLLLL GAGESGKSTI VKQMKIIHEA GYSEEECKQY KAVVYSNTIQ SIIAIIRAM GRLKIDFGDS ARADDARQLF VLAGAAEEGF MTAELAGVIK RLWKDSGVQA CFNRSREYQL NDSAAYYLND L DRIAQPNY IPTQQDVLRT RVKTTGIVET HFTFKDLHFK MFDVGGQRSE RKKWIHCFEG VTAIIFCVAL SDYDLVLAED EE MNRMHES MKLFDSICNN KWFTDTSIIL FLNKKDLFEE KIKKSPLTIC YPEYAGSNTY EEAAAYIQCQ FEDLNKRKDT KEI YTHFTC ATDTKNVQFV FDAVTDVIIK NNLKDCGLF

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Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.728152 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD ...String:
GPGSSGSELD QLRQEAEQLK NQIRDARKAC ADATLSQITN NIDPVGRIQM RTRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDS YTTNKVHAIP LRSSWVMTCA YAPSGNYVAC GGLDNICSIY NLKTREGNVR VSRELAGHTG YLSCCRFLDD N QIVTSSGD TTCALWDIET GQQTTTFTGH TGDVMSLSLA PDTRLFVSGA CDASAKLWDV REGMCRQTFT GHESDINAIC FF PNGNAFA TGSDDATCRL FDLRADQELM TYSHDNIICG ITSVSFSKSG RLLLAGYDDF NCNVWDALKA DRAGVLAGHD NRV SCLGVT DDGMAVATGS WDSFLKIWN

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Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.845078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFSAI L

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Macromolecule #6: single-chain antibody Fv fragment (scFv16)

MacromoleculeName: single-chain antibody Fv fragment (scFv16) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.784896 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAHHHHHH HH

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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: 8
Component:
ConcentrationFormulaName
20.0 mMHEPEShydroxyethyl piperazine ethane sulfonicacid
150.0 mMNaClsodium chloride
0.01 %GDNglyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / 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 / Cs: 0.1 mm / Nominal defocus max: 3.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 75000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1339224
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2.0)
Startup modelType of model: OTHER
Details: Initial 3D volume generated by ab initio reconstruction was used as startup model.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 233117
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)

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Atomic model buiding 1

Initial model
PDB IDChain

5zbh

chain_id: A

6os9

chain_id: A

6os9

chain_id: B

6os9

chain_id: C

6os9

chain_id: D
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7vgx:
Neuropeptide Y Y1 Receptor (NPY1R) in Complex with G Protein and its endogeneous Peptide-Agonist Neuropeptide Y (NPY)

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