[English] 日本語
Yorodumi- EMDB-21249: Cryo-EM structure of an activated VIP1 receptor-G protein complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21249 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of an activated VIP1 receptor-G protein complex | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / NGF-independant TRKA activation / regulation of G protein-coupled receptor signaling pathway / neuropeptide hormone activity / G protein-coupled peptide receptor activity / insulin secretion / peptide hormone receptor binding ...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 / NGF-independant TRKA activation / regulation of G protein-coupled receptor signaling pathway / neuropeptide hormone activity / G protein-coupled peptide receptor activity / insulin secretion / peptide hormone receptor binding / activation of adenylate cyclase activity / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of cell cycle / neuropeptide signaling pathway / positive regulation of protein kinase activity / cAMP-mediated signaling / positive regulation of GTPase activity / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / 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 / G beta:gamma signalling through CDC42 / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / neuron projection development / positive regulation of cold-induced thermogenesis / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / cell-cell signaling / GTPase binding / regulation of protein localization / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / perikaryon / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / positive regulation of ERK1 and ERK2 cascade / receptor complex / cell surface receptor signaling pathway / neuron projection / G protein-coupled receptor signaling pathway / lysosomal membrane / signaling receptor binding / GTPase activity / positive regulation of cell population proliferation / synapse / protein-containing complex binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Duan J / Shen D-D / Zhou XE / Liu Q-F / Zhuang Y-W / Zhang H-B / Xu P-Y / Ma S-S / He X-H / Melcher K ...Duan J / Shen D-D / Zhou XE / Liu Q-F / Zhuang Y-W / Zhang H-B / Xu P-Y / Ma S-S / He X-H / Melcher K / Zhang Y / Xu HE / Yi J | |||||||||
Funding support | China, 2 items
| |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of an activated VIP1 receptor-G protein complex revealed by a NanoBiT tethering strategy. Authors: Jia Duan / Dan-Dan Shen / X Edward Zhou / Peng Bi / Qiu-Feng Liu / Yang-Xia Tan / You-Wen Zhuang / Hui-Bing Zhang / Pei-Yu Xu / Si-Jie Huang / Shan-Shan Ma / Xin-Heng He / Karsten Melcher / ...Authors: Jia Duan / Dan-Dan Shen / X Edward Zhou / Peng Bi / Qiu-Feng Liu / Yang-Xia Tan / You-Wen Zhuang / Hui-Bing Zhang / Pei-Yu Xu / Si-Jie Huang / Shan-Shan Ma / Xin-Heng He / Karsten Melcher / Yan Zhang / H Eric Xu / Yi Jiang / Abstract: Vasoactive intestinal polypeptide receptor (VIP1R) is a widely expressed class B G protein-coupled receptor and a drug target for the treatment of neuronal, metabolic, and inflammatory diseases. ...Vasoactive intestinal polypeptide receptor (VIP1R) is a widely expressed class B G protein-coupled receptor and a drug target for the treatment of neuronal, metabolic, and inflammatory diseases. However, our understanding of its mechanism of action and the potential of drug discovery targeting this receptor is limited by the lack of structural information of VIP1R. Here we report a cryo-electron microscopy structure of human VIP1R bound to PACAP27 and Gs heterotrimer, whose complex assembly is stabilized by a NanoBiT tethering strategy. Comparison with other class B GPCR structures reveals that PACAP27 engages VIP1R with its N-terminus inserting into the ligand binding pocket at the transmembrane bundle of the receptor, which subsequently couples to the G protein in a receptor-specific manner. This structure has provided insights into the molecular basis of PACAP27 binding and VIP receptor activation. The methodology of the NanoBiT tethering may help to provide structural information of unstable complexes. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21249.map.gz | 38 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21249-v30.xml emd-21249.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
Images | emd_21249.png | 50.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21249 | HTTPS FTP |
-Validation report
Summary document | emd_21249_validation.pdf.gz | 449.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_21249_full_validation.pdf.gz | 449.2 KB | Display | |
Data in XML | emd_21249_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | emd_21249_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21249 | HTTPS FTP |
-Related structure data
Related structure data | 6vn7MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21249.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : PACAP27-VIP1R-Gs protein complex stabilized by Nanobody 35 and Na...
Entire | Name: PACAP27-VIP1R-Gs protein complex stabilized by Nanobody 35 and NanoBiT system |
---|---|
Components |
|
-Supramolecule #1: PACAP27-VIP1R-Gs protein complex stabilized by Nanobody 35 and Na...
Supramolecule | Name: PACAP27-VIP1R-Gs protein complex stabilized by Nanobody 35 and NanoBiT system type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
-Macromolecule #1: Vasoactive intestinal polypeptide receptor 1
Macromolecule | Name: Vasoactive intestinal polypeptide receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 66.245188 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: DYKDDDDVDH HHHHHHHARL QEECDYVQMI EVQHKQCLEE AQLENETIGC SKMWDNLTCW PATPRGQVVV LACPLIFKLF SSIQGRNVS RSCTDEGWTH LEPGPYPIAC GLDDKAASLD EQQTMFYGSV KTGYTIGYGL SLATLLVATA ILSLFRKLHC T RNYIHMHL ...String: DYKDDDDVDH HHHHHHHARL QEECDYVQMI EVQHKQCLEE AQLENETIGC SKMWDNLTCW PATPRGQVVV LACPLIFKLF SSIQGRNVS RSCTDEGWTH LEPGPYPIAC GLDDKAASLD EQQTMFYGSV KTGYTIGYGL SLATLLVATA ILSLFRKLHC T RNYIHMHL FISFILRAAA VFIKDLALFD SGESDQCSEG SVGCKAAMVF FQYCVMANFF WLLVEGLYLY TLLAVSFFSE RK YFWGYIL IGWGVPSTFT MVWTIARIHF EDYGCWDTIN SSLWWIIKGP ILTSILVNFI LFICIIRILL QKLRPPDIRK SDS SPYSRL ARSTLLLIPL FGVHYIMFAF FPDNFKPEVK MVFELVVGSF QGFVVAILYC FLNGEVQAEL RRKWRRWHLQ GVLG WNPKY RHPSGGSNGA TCSTQVSMLV FTLEDFVGDW EQTAAYNLDQ VLEQGGVSSL LQNLAVSVTP IQRIVRSGEN ALKID IHVI IPYEGLSADQ MAQIEEVFKV VYPVDDHHFK VILPYGTLVI DGVTPNMLNY FGRPYEGIAV FDGKKITVTG TLWNGN KII DERLITPDGS MLFRVTINS |
-Macromolecule #2: Pituitary adenylate cyclase-activating polypeptide
Macromolecule | Name: Pituitary adenylate cyclase-activating polypeptide / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.154642 KDa |
Sequence | String: HSDGIFTDSY SRYRKQMAVK KYLAAVL |
-Macromolecule #3: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 45.727441 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: 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 weight | Theoretical: 41.055867 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 LKIWNGSSGG GGSGGGGSSG VSGWRLFKKI S |
-Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: 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 weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L |
-Macromolecule #6: Nanobody 35
Macromolecule | Name: Nanobody 35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.71432 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHH |
-Macromolecule #7: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 6 / Formula: CLR |
---|---|
Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ChemComp-CLR: |
-Macromolecule #8: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 8 / Number of copies: 4 / Formula: PLM |
---|---|
Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131263 |
---|---|
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |