[English] 日本語
Yorodumi- EMDB-7039: 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bo... -
+
Open data
-
Basic information
| Entry | Database: EMDB / ID: EMD-7039 | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | 3.3 angstrom phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex. | |||||||||||||||
Map data | Sharpened map of a biased agonist-bound human GLP-1 receptor-Gs complex | |||||||||||||||
Sample |
| |||||||||||||||
Keywords | class B G protein-coupled receptor / agonist-receptor-G protein ternary complex / glucagon-like peptide 1 receptor / active-state G protein-coupled receptor / signaling protein / phase plate / phase contrast / single particle cryo-em | |||||||||||||||
| Function / homology | Function and homology informationglucagon-like peptide 1 receptor activity / glucagon receptor activity / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / PKA activation in glucagon signalling / developmental growth ...glucagon-like peptide 1 receptor activity / glucagon receptor activity / positive regulation of blood pressure / hormone secretion / post-translational protein targeting to membrane, translocation / response to psychosocial stress / regulation of heart contraction / peptide hormone binding / PKA activation in glucagon signalling / developmental growth / hair follicle placode formation / D1 dopamine receptor binding / intracellular transport / vascular endothelial cell response to laminar fluid shear stress / renal water homeostasis / activation of adenylate cyclase activity / Hedgehog 'off' state / negative regulation of blood pressure / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to glucagon stimulus / regulation of insulin secretion / adenylate cyclase activator activity / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / bone development / platelet aggregation / G-protein beta/gamma-subunit complex binding / cognition / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / 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 / sensory perception of smell / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / transmembrane signaling receptor activity / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / 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) / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / G protein activity / positive regulation of cytosolic calcium ion concentration / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Ras protein signal transduction / learning or memory / cell surface receptor signaling pathway / Extra-nuclear estrogen signaling / cell population proliferation / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / GTP binding / protein-containing complex binding / signal transduction / extracellular exosome / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) / synthetic construct (others) / ![]() | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Liang YL / Khoshouei M | |||||||||||||||
| Funding support | Australia, 4 items
| |||||||||||||||
Citation | Journal: Nature / Year: 2018Title: Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor-Gs complex. Authors: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia ...Authors: Yi-Lynn Liang / Maryam Khoshouei / Alisa Glukhova / Sebastian G B Furness / Peishen Zhao / Lachlan Clydesdale / Cassandra Koole / Tin T Truong / David M Thal / Saifei Lei / Mazdak Radjainia / Radostin Danev / Wolfgang Baumeister / Ming-Wei Wang / Laurence J Miller / Arthur Christopoulos / Patrick M Sexton / Denise Wootten / ![]() Abstract: The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism- ...The class B glucagon-like peptide-1 (GLP-1) G protein-coupled receptor is a major target for the treatment of type 2 diabetes and obesity. Endogenous and mimetic GLP-1 peptides exhibit biased agonism-a difference in functional selectivity-that may provide improved therapeutic outcomes. Here we describe the structure of the human GLP-1 receptor in complex with the G protein-biased peptide exendin-P5 and a Gα heterotrimer, determined at a global resolution of 3.3 Å. At the extracellular surface, the organization of extracellular loop 3 and proximal transmembrane segments differs between our exendin-P5-bound structure and previous GLP-1-bound GLP-1 receptor structure. At the intracellular face, there was a six-degree difference in the angle of the Gαs-α5 helix engagement between structures, which was propagated across the G protein heterotrimer. In addition, the structures differed in the rate and extent of conformational reorganization of the Gα protein. Our structure provides insights into the molecular basis of biased agonism. | |||||||||||||||
| History |
|
-
Structure visualization
| Movie |
Movie viewer |
|---|---|
| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
-
Downloads & links
-EMDB archive
| Map data | emd_7039.map.gz | 4.8 MB | EMDB map data format | |
|---|---|---|---|---|
| Header (meta data) | emd-7039-v30.xml emd-7039.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_7039_fsc.xml | 7.1 KB | Display | FSC data file |
| Images | emd_7039.png | 462.3 KB | ||
| Filedesc metadata | emd-7039.cif.gz | 7.5 KB | ||
| Others | emd_7039_half_map_1.map.gz emd_7039_half_map_2.map.gz | 23.4 MB 23.4 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7039 | HTTPS FTP |
-Validation report
| Summary document | emd_7039_validation.pdf.gz | 704 KB | Display | EMDB validaton report |
|---|---|---|---|---|
| Full document | emd_7039_full_validation.pdf.gz | 703.5 KB | Display | |
| Data in XML | emd_7039_validation.xml.gz | 12.8 KB | Display | |
| Data in CIF | emd_7039_validation.cif.gz | 17.9 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7039 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7039 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6b3jMC M: atomic model generated by this map C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
|---|---|
| Related items in Molecule of the Month |
-
Map
| File | Download / File: emd_7039.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Sharpened map of a biased agonist-bound human GLP-1 receptor-Gs complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
CCP4 map header:
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-Supplemental data
-Half map: Unfil half1 map of a biased agonist-bound human...
| File | emd_7039_half_map_1.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Unfil half1 map of a biased agonist-bound human GLP-1 receptor-Gs complex | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-Half map: Unfil half2 map of a biased agonist-bound human...
| File | emd_7039_half_map_2.map | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Annotation | Unfil half2 map of a biased agonist-bound human GLP-1 receptor-Gs complex | ||||||||||||
| Projections & Slices |
| ||||||||||||
| Density Histograms |
-
Sample components
-Entire : Complex of a full-length, active-state glucagon-like peptide-1 re...
| Entire | Name: Complex of a full-length, active-state glucagon-like peptide-1 receptor with exendin-P5 ligand, heterotrimeric Gs protein and nanobody 35. |
|---|---|
| Components |
|
-Supramolecule #1: Complex of a full-length, active-state glucagon-like peptide-1 re...
| Supramolecule | Name: Complex of a full-length, active-state glucagon-like peptide-1 receptor with exendin-P5 ligand, heterotrimeric Gs protein and nanobody 35. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
|---|---|
| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Glucagon-like peptide 1 receptor
| Macromolecule | Name: Glucagon-like peptide 1 receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
|---|---|
| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 56.748418 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| Sequence | String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PARPQGATVS LWETVQKWRE YRRQCQRSLT EDPPPATDLF CNRTFDEYAC WPDGEPGSF VNVSCPWYLP WASSVPQGHV YRFCTAEGLW LQKDNSSLPW RDLSECEESK RGERSSPEEQ LLFLYIIYTV G YALSFSAL ...String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PARPQGATVS LWETVQKWRE YRRQCQRSLT EDPPPATDLF CNRTFDEYAC WPDGEPGSF VNVSCPWYLP WASSVPQGHV YRFCTAEGLW LQKDNSSLPW RDLSECEESK RGERSSPEEQ LLFLYIIYTV G YALSFSAL VIASAILLGF RHLHCTRNYI HLNLFASFIL RALSVFIKDA ALKWMYSTAA QQHQWDGLLS YQDSLSCRLV FL LMQYCVA ANYYWLLVEG VYLYTLLAFS VFSEQWIFRL YVSIGWGVPL LFVVPWGIVK YLYEDEGCWT RNSNMNYWLI IRL PILFAI GVNFLIFVRV ICIVVSKLKA NLMCKTDIKC RLAKSTLTLI PLLGTHEVIF AFVMDEHARG TLRFIKLFTE LSFT SFQGL MVAILYCFVN NEVQLEFRKS WERWRLEHLH IQRDSSMKPL KCPTSSLSSG ATAGSSMYTA TCQASCSPAG LEVLF QGPH HHHHHHH UniProtKB: Glucagon-like peptide 1 receptor |
-Macromolecule #2: Exendin-P5
| Macromolecule | Name: Exendin-P5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
|---|---|
| Source (natural) | Organism: synthetic construct (others) |
| Molecular weight | Theoretical: 4.22867 KDa |
| Sequence | String: ELVDNAVGGD LSKQMEEEAV RLFIEWLKNG GPSSGAPPPS |
-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: 45.683434 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| 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 LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ AALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
-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: 38.534062 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| Sequence | String: MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV ...String: MHHHHHHGSS GSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKL IIWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC R FLDDNQIV TSSGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD IN AICFFPN GNAFATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAG HDNRVS CLGVTDDGMA VATGSWDSFL KIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-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: Trichoplusia ni (cabbage looper) |
| Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #6: Nanobody 35
| Macromolecule | Name: Nanobody 35 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
|---|---|
| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 15.140742 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEA |
-Experimental details
-Structure determination
| Method | cryo EM |
|---|---|
Processing | single particle reconstruction |
| Aggregation state | particle |
-
Sample preparation
| Concentration | 0.3 mg/mL |
|---|---|
| Buffer | pH: 7.5 |
| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
| Microscope | FEI TITAN KRIOS |
|---|---|
| Specialist optics | Energy filter - Name: Gatan Quantum energy filter |
| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 2793 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 47170 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
+
Image processing
-Atomic model buiding 1
| Initial model |
| ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Details | 3C5T was rigid body fitted with minimal manual adjustments. The rest of the chain R and chains A,B,G,N were extensively remodeled. Chain P was built de novo. | ||||||||||||||
| Output model | ![]() PDB-6b3j: |
Movie
Controller
About Yorodumi


Keywords
Homo sapiens (human)
Authors
Australia, 4 items
Citation

UCSF Chimera



























Z (Sec.)
Y (Row.)
X (Col.)





































Trichoplusia ni (cabbage looper)





