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- EMDB-32095: Cryo-EM structure of human vasoactive intestinal polypeptide rece... -

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Entry
Database: EMDB / ID: EMD-32095
TitleCryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs
Map data
Sample
  • Complex: Cryo-EM structure of the human vasoactive intestinal polypeptide receptor 2 in commplex with PACAP27 and G protein
    • Complex: human vasoactive intestinal polypeptide receptor 2
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Pituitary adenylate cyclase activating peptide-27
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Guanine nucleotide-binding protein G(I) /G(S) /G(T) subunit beta-1
      • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide 27Pituitary adenylate cyclase-activating peptide
    • Complex: Guanine nucleotide-binding protein G(I) /G(S) /G(O) subunit gamma-2
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Nanobody-35Single-domain antibody
      • Protein or peptide: Vasoactive intestinal polypeptide receptor 2
Function / homology
Function and homology information


pituitary adenylate cyclase activating polypeptide activity / vasoactive intestinal polypeptide receptor activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / sensory perception of chemical stimulus / mu-type opioid receptor binding / NGF-independant TRKA activation / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / regulation of G protein-coupled receptor signaling pathway ...pituitary adenylate cyclase activating polypeptide activity / vasoactive intestinal polypeptide receptor activity / positive regulation of chemokine (C-C motif) ligand 5 production / positive regulation of growth hormone secretion / sensory perception of chemical stimulus / mu-type opioid receptor binding / NGF-independant TRKA activation / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / regulation of G protein-coupled receptor signaling pathway / G-protein activation / Activation of the phototransduction cascade / : / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Activation of G protein gated Potassium channels / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (z) signalling events / G protein-coupled peptide receptor activity / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / G alpha (i) signalling events / Thrombin signalling through proteinase activated receptors (PARs) / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / alkylglycerophosphoethanolamine phosphodiesterase activity / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / insulin secretion / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / beta-2 adrenergic receptor binding / G alpha (q) signalling events / peptide hormone receptor binding / photoreceptor outer segment membrane / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / spectrin binding / Vasopressin regulates renal water homeostasis via Aquaporins / peptide hormone binding / cAMP-mediated signaling / negative regulation of cell cycle / photoreceptor outer segment / D1 dopamine receptor binding / neuropeptide signaling pathway / positive regulation of protein kinase activity / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / cardiac muscle cell apoptotic process / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / activation of adenylate cyclase activity / photoreceptor inner segment / adenylate cyclase activator activity / female pregnancy / G protein-coupled receptor activity / negative regulation of smooth muscle cell proliferation / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Glucagon-type ligand receptors / positive regulation of GTPase activity / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / sensory perception of taste / neuron projection development / G-protein beta-subunit binding / heterotrimeric G-protein complex / regulation of protein localization / signaling receptor complex adaptor activity / retina development in camera-type eye / cell-cell signaling / GTPase binding / cell body / phospholipase C-activating G protein-coupled receptor signaling pathway
Similarity search - Function
GPCR, family 2, vasoactive intestinal peptide receptor 2 / : / GPCR, family 2, vasoactive intestinal peptide receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain ...GPCR, family 2, vasoactive intestinal peptide receptor 2 / : / GPCR, family 2, vasoactive intestinal peptide receptor / : / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / G-protein coupled receptors family 2 signature 1. / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein alpha subunit, group S / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / GGL domain / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Pituitary adenylate cyclase-activating polypeptide / Vasoactive intestinal polypeptide receptor 2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesBos taurus (cattle) / Homo sapiens (human) / synthetic construct (others) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsXu YN / Feng WB / Zhou QT / Liang AY / Li J / Dai AT / Zhao FH / Yan JH / Chen CW / Li H ...Xu YN / Feng WB / Zhou QT / Liang AY / Li J / Dai AT / Zhao FH / Yan JH / Chen CW / Li H / Zhao LH / Xia T / Jiang Y / Xu HE / Yang DH / Wang MW
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81872915 China
National Natural Science Foundation of China (NSFC)82073904 China
National Natural Science Foundation of China (NSFC)81773792 China
National Natural Science Foundation of China (NSFC)81973373 China
National Natural Science Foundation of China (NSFC)21704064 China
CitationJournal: Nat Commun / Year: 2022
Title: A distinctive ligand recognition mechanism by the human vasoactive intestinal polypeptide receptor 2.
Authors: Yingna Xu / Wenbo Feng / Qingtong Zhou / Anyi Liang / Jie Li / Antao Dai / Fenghui Zhao / Jiahui Yan / Chuan-Wei Chen / Hao Li / Li-Hua Zhao / Tian Xia / Yi Jiang / H Eric Xu / Dehua Yang / Ming-Wei Wang /
Abstract: Class B1 of G protein-coupled receptors (GPCRs) comprises 15 members activated by physiologically important peptide hormones. Among them, vasoactive intestinal polypeptide receptor 2 (VIP2R) is ...Class B1 of G protein-coupled receptors (GPCRs) comprises 15 members activated by physiologically important peptide hormones. Among them, vasoactive intestinal polypeptide receptor 2 (VIP2R) is expressed in the central and peripheral nervous systems and involved in a number of pathophysiological conditions, including pulmonary arterial hypertension, autoimmune and psychiatric disorders, in which it is thus a valuable drug target. Here, we report the cryo-electron microscopy structure of the human VIP2R bound to its endogenous ligand PACAP27 and the stimulatory G protein. Different from all reported peptide-bound class B1 GPCR structures, the N-terminal α-helix of VIP2R adopts a unique conformation that deeply inserts into a cleft between PACAP27 and the extracellular loop 1, thereby stabilizing the peptide-receptor interface. Its truncation or extension significantly decreased VIP2R-mediated cAMP accumulation. Our results provide additional information on peptide recognition and receptor activation among class B1 GPCRs and may facilitate the design of better therapeutics.
History
DepositionOct 21, 2021-
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_32095.png

Downloads & links

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Map

FileDownload / File: emd_32095.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.071 Å
Density
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-2.9917812 - 4.646252
Average (Standard dev.)-0.00076792075 (±0.07675719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of the human vasoactive intestinal polypeptide ...

EntireName: Cryo-EM structure of the human vasoactive intestinal polypeptide receptor 2 in commplex with PACAP27 and G protein
Components
  • Complex: Cryo-EM structure of the human vasoactive intestinal polypeptide receptor 2 in commplex with PACAP27 and G protein
    • Complex: human vasoactive intestinal polypeptide receptor 2
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
    • Complex: Pituitary adenylate cyclase activating peptide-27
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: Guanine nucleotide-binding protein G(I) /G(S) /G(T) subunit beta-1
      • Protein or peptide: Pituitary adenylate cyclase-activating polypeptide 27Pituitary adenylate cyclase-activating peptide
    • Complex: Guanine nucleotide-binding protein G(I) /G(S) /G(O) subunit gamma-2
      • Protein or peptide: Nanobody-35Single-domain antibody
    • Complex: Nanobody-35Single-domain antibody
      • Protein or peptide: Vasoactive intestinal polypeptide receptor 2

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Supramolecule #1: Cryo-EM structure of the human vasoactive intestinal polypeptide ...

SupramoleculeName: Cryo-EM structure of the human vasoactive intestinal polypeptide receptor 2 in commplex with PACAP27 and G protein
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bos taurus (cattle)

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Supramolecule #2: human vasoactive intestinal polypeptide receptor 2

SupramoleculeName: human vasoactive intestinal polypeptide receptor 2 / type: complex / Chimera: Yes / 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: Pituitary adenylate cyclase activating peptide-27

SupramoleculeName: Pituitary adenylate cyclase activating peptide-27 / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: complex / Chimera: Yes / ID: 4 / Parent: 1 / Macromolecule list: #3

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Supramolecule #5: Guanine nucleotide-binding protein G(I) /G(S) /G(T) subunit beta-1

SupramoleculeName: Guanine nucleotide-binding protein G(I) /G(S) /G(T) subunit beta-1
type: complex / Chimera: Yes / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)

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Supramolecule #6: Guanine nucleotide-binding protein G(I) /G(S) /G(O) subunit gamma-2

SupramoleculeName: Guanine nucleotide-binding protein G(I) /G(S) /G(O) subunit gamma-2
type: complex / Chimera: Yes / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #7: Nanobody-35

SupramoleculeName: Nanobody-35 / type: complex / Chimera: Yes / ID: 7 / Parent: 1 / Macromolecule list: #6

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Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 45.743441 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQD DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ AALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCS VDTENIRRVF NDCRDIIQRM HLRQYELL

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.70675 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MHHHHHHSSG LVPRGSHMAS HHHHHHHHHH GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN L KTREGNVR ...String:
MHHHHHHSSG LVPRGSHMAS HHHHHHHHHH GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHL AKIYAMHWGT DSRLLVSASQ DGKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN L KTREGNVR VSRELAGHTG YLSCCRFLDD NQIVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DA SAKLWDV REGMCRQTFT GHESDINAIC FFPNGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLL AGYDDF NCNVWDALKA DRAGVLAGHD NRVSCLGVTD DGMAVATGSW DSFLKIWNGS SGGGGSGGGG SSGVSGWRLF KKIS

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Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

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Macromolecule #4: Pituitary adenylate cyclase-activating polypeptide 27

MacromoleculeName: Pituitary adenylate cyclase-activating polypeptide 27 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.154642 KDa
SequenceString:
HSDGIFTDSY SRYRKQMAVK KYLAAVL

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Macromolecule #5: Nanobody-35

MacromoleculeName: Nanobody-35 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.343019 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAQVQLQESG GGLVQPGGSL RLSCAASGFT FSNYKMNWVR QAPGKGLEWV SDISQSGASI SYTGSVKGRF TISRDNAKNT LYLQMNSLK PEDTAVYYCA RCPAPFTRDC FDVTSTTYAY RGQGTQVTVS SHHHHHHEPE A

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Macromolecule #6: Vasoactive intestinal polypeptide receptor 2

MacromoleculeName: Vasoactive intestinal polypeptide receptor 2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.579445 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ECRFHLEIQE EETKCAELLR SQTEKHKACS GVWDNITCWR PANVGETVTV PCPKVFSNFY SKAGNISKNC TSDGWSETFP DFVDACGYS DPEDESKITF YILVKAIYTL GYSVSLMSLA TGSIILCLFR KLHCTRNYIH LNLFLSFILR AISVLVKDDV L YSSSGTLH ...String:
ECRFHLEIQE EETKCAELLR SQTEKHKACS GVWDNITCWR PANVGETVTV PCPKVFSNFY SKAGNISKNC TSDGWSETFP DFVDACGYS DPEDESKITF YILVKAIYTL GYSVSLMSLA TGSIILCLFR KLHCTRNYIH LNLFLSFILR AISVLVKDDV L YSSSGTLH CPDQPSSWVG CKLSLVFLQY CIMANFFWLL VEGLYLHTLL VAMLPPRRCF LAYLLIGWGL PTVCIGAWTA AR LYLEDTG CWDTNDHSVP WWVIRIPILI SIIVNFVLFI SIIRILLQKL TSPDVGGNDQ SQYKRLAKST LLLIPLFGVH YMV FAVFPI SISSKYQILF ELCLGSFQGL VVAVLYCFLN SEVQCELKRK WRSRCPTPSA SRDYRVCGSS FSRNGSEGAL QFHR GSRAQ SFLQTETSVI VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEG LSAD QMAQIEEVFK VVYPVDDHHF KVILPYGTLV IDGVTPNMLN YFGRPYEGIA VFDGKKITVT GTLWNGNKII DERLIT PDG SMLFRVTINS

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2x57

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Number images used: 602466

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