[English] 日本語
Yorodumi- EMDB-36342: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36342 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | complex / chimera / GPCR / membrane protein | |||||||||
Function / homology | Function and homology information beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / positive regulation of cAMP-dependent protein kinase activity / positive regulation of AMPA receptor activity / norepinephrine binding / Adrenoceptors / heat generation / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / response to psychosocial stress / negative regulation of multicellular organism growth / negative regulation of G protein-coupled receptor signaling pathway / adrenergic receptor signaling pathway / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of protein kinase A signaling / adenylate cyclase binding / smooth muscle contraction / potassium channel regulator activity / bone resorption / positive regulation of bone mineralization / adenylate cyclase-activating adrenergic receptor signaling pathway / brown fat cell differentiation / regulation of sodium ion transport / response to cold / receptor-mediated endocytosis / electron transport chain / clathrin-coated endocytic vesicle membrane / positive regulation of protein serine/threonine kinase activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G alpha (s) signalling events / transcription by RNA polymerase II / positive regulation of MAPK cascade / periplasmic space / electron transfer activity / early endosome / lysosome / cell surface receptor signaling pathway / receptor complex / endosome membrane / Ub-specific processing proteases / endosome / iron ion binding / apical plasma membrane / heme binding / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | He BB / Zhong YX / Guo Q / Tao YY | |||||||||
Funding support | China, 1 items
| |||||||||
Citation | Journal: Nat Chem Biol / Year: 2024 Title: A method for structure determination of GPCRs in various states. Authors: Qiong Guo / Binbin He / Yixuan Zhong / Haizhan Jiao / Yinhang Ren / Qinggong Wang / Qiangqiang Ge / Yongxiang Gao / Xiangyu Liu / Yang Du / Hongli Hu / Yuyong Tao / Abstract: G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by ...G-protein-coupled receptors (GPCRs) are a class of integral membrane proteins that detect environmental cues and trigger cellular responses. Deciphering the functional states of GPCRs induced by various ligands has been one of the primary goals in the field. Here we developed an effective universal method for GPCR cryo-electron microscopy structure determination without the need to prepare GPCR-signaling protein complexes. Using this method, we successfully solved the structures of the β-adrenergic receptor (βAR) bound to antagonistic and agonistic ligands and the adhesion GPCR ADGRL3 in the apo state. For βAR, an intermediate state stabilized by the partial agonist was captured. For ADGRL3, the structure revealed that inactive ADGRL3 adopts a compact fold and that large unusual conformational changes on both the extracellular and intracellular sides are required for activation of adhesion GPCRs. We anticipate that this method will open a new avenue for understanding GPCR structure‒function relationships and drug development. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_36342.map.gz | 79 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-36342-v30.xml emd-36342.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36342_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_36342.png | 97.3 KB | ||
Filedesc metadata | emd-36342.cif.gz | 5.7 KB | ||
Others | emd_36342_half_map_1.map.gz emd_36342_half_map_2.map.gz | 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36342 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36342 | HTTPS FTP |
-Related structure data
Related structure data | 8jj8MC 8j7eC 8jjlC 8jjoC 8jmtC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_36342.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_36342_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_36342_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with ...
Entire | Name: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with ...
Supramolecule | Name: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Beta-2 adrenergic receptor,Soluble cytochrome b562
Macromolecule | Name: Beta-2 adrenergic receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 51.594102 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDKDEVWVV GMGIVMSLIV LAIVFGNVLV ITAIAKFERL QTVTNYFITS LACADLVMGL AVVPFGAAH ILMKMWTFGN FWCEFWTSID VLCVTASIET LCVIAVDRYF AITSPFKYQS LLTKNKARVI ILMVWIVSGL T SFLPIQMH ...String: MKTIIALSYI FCLVFADYKD DDDKDEVWVV GMGIVMSLIV LAIVFGNVLV ITAIAKFERL QTVTNYFITS LACADLVMGL AVVPFGAAH ILMKMWTFGN FWCEFWTSID VLCVTASIET LCVIAVDRYF AITSPFKYQS LLTKNKARVI ILMVWIVSGL T SFLPIQMH WYRATHQEAI NCYAEETCCD FFTNQAYAIA SSIVSFYVPL VIMVFVYSRV FQEAKRQLAD LEDNWETLND NL KVIEKAD NAAQVKDALT KMRAAALDAQ KASGSGSPEM KDFRHGFDIL VGQIDDALKL ANEGKVKEAQ AAAEQLKTTR NAY IQKYLK FCLKEHKALK TLGIIMGTFT LCWLPFFIVN IVHVIQDNLI RKEVYILLNW IGYVNSGFNP LIYSRSPDFR IAFQ ELLKI AALKEKIAAL KEKIAALKEA EEKRASRLEE ELRRRLTEGS HHHHHHHH UniProtKB: Beta-2 adrenergic receptor, Soluble cytochrome b562, Beta-2 adrenergic receptor |
-Macromolecule #2: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino...
Macromolecule | Name: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide type: ligand / ID: 2 / Number of copies: 1 / Formula: H98 |
---|---|
Molecular weight | Theoretical: 344.405 Da |
Chemical component information | ChemComp-H98: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Material: NICKEL/TITANIUM |
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |