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- EMDB-36361: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36361
TitleCryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with an antagonist
Map data
Sample
  • Complex: chimeric beta-2 adrenergic receptor
    • Protein or peptide: Beta-2 adrenergic receptor,Beta-2 adrenergic receptor,Soluble cytochrome b562
  • Ligand: (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol
Keywordscomplex / Membrane protein
Function / homology
Function and homology information


positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction ...positive regulation of mini excitatory postsynaptic potential / beta2-adrenergic receptor activity / AMPA selective glutamate receptor signaling pathway / norepinephrine binding / positive regulation of autophagosome maturation / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / heat generation / Adrenoceptors / activation of transmembrane receptor protein tyrosine kinase activity / negative regulation of smooth muscle contraction / positive regulation of lipophagy / negative regulation of G protein-coupled receptor signaling pathway / negative regulation of multicellular organism growth / adrenergic receptor signaling pathway / response to psychosocial stress / endosome to lysosome transport / diet induced thermogenesis / neuronal dense core vesicle / positive regulation of cAMP/PKA signal transduction / adenylate cyclase binding / smooth muscle contraction / bone resorption / positive regulation of bone mineralization / potassium channel regulator activity / brown fat cell differentiation / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / receptor-mediated endocytosis / response to cold / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / amyloid-beta binding / positive regulation of cold-induced thermogenesis / microtubule cytoskeleton / G alpha (s) signalling events / transcription by RNA polymerase II / early endosome / lysosome / receptor complex / cell surface receptor signaling pathway / positive regulation of MAPK cascade / endosome / endosome membrane / Ub-specific processing proteases / ciliary basal body / cilium / apical plasma membrane / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / membrane / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Serpentine type 7TM GPCR chemoreceptor Srsx / 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)
Similarity search - Domain/homology
Beta-2 adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHe BB / Zhong YX / Guo Q / Tao YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMay 31, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36361.png

Downloads & links

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Map

FileDownload / File: emd_36361.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 220 pix.
= 235.4 Å		1.07 Å/pix.
x 220 pix.
= 235.4 Å		1.07 Å/pix.
x 220 pix.
= 235.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.924
Minimum - Maximum-5.9328055 - 7.50582
Average (Standard dev.)-0.0019967356 (±0.15822047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 235.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36361_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #1

Fileemd_36361_half_map_2.map
Projections & Slices
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Sample components

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Entire : chimeric beta-2 adrenergic receptor

EntireName: chimeric beta-2 adrenergic receptor
Components
  • Complex: chimeric beta-2 adrenergic receptor
    • Protein or peptide: Beta-2 adrenergic receptor,Beta-2 adrenergic receptor,Soluble cytochrome b562
  • Ligand: (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol

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Supramolecule #1: chimeric beta-2 adrenergic receptor

SupramoleculeName: chimeric beta-2 adrenergic receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-2 adrenergic receptor,Beta-2 adrenergic receptor,Soluble cyt...

MacromoleculeName: Beta-2 adrenergic receptor,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 weightTheoretical: 51.594102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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, Beta-2 adrenergic receptor

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Macromolecule #2: (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol

MacromoleculeName: (2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol
type: ligand / ID: 2 / Number of copies: 1 / Formula: JTZ
Molecular weightTheoretical: 249.349 Da
Chemical component information

ChemComp-JTZ:
(2S)-1-[(1-methylethyl)amino]-3-(2-prop-2-en-1-ylphenoxy)propan-2-ol

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
GridMaterial: NICKEL/TITANIUM / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 173740
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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