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- EMDB-36342: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-36342
TitleCryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist
Map data
Sample
  • Complex: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist
    • Protein or peptide: Beta-2 adrenergic receptor,Soluble cytochrome b562
  • Ligand: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide
Keywordscomplex / chimera / GPCR / membrane protein
Function / homology
Function and homology information


beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction ...beta2-adrenergic receptor activity / positive regulation of mini excitatory postsynaptic potential / AMPA selective glutamate receptor signaling pathway / norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / positive regulation of autophagosome maturation / heat generation / norepinephrine binding / Adrenoceptors / negative regulation of smooth muscle contraction / positive regulation of cardiac muscle cell 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 / diet induced thermogenesis / endosome to lysosome transport / positive regulation of cAMP/PKA signal transduction / smooth muscle contraction / adenylate cyclase binding / negative regulation of cardiac muscle cell apoptotic process / potassium channel regulator activity / positive regulation of bone mineralization / bone resorption / neuronal dense core vesicle / intercellular bridge / regulation of sodium ion transport / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of cardiac muscle cell apoptotic process / receptor-mediated endocytosis / brown fat cell differentiation / response to cold / clathrin-coated endocytic vesicle membrane / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / cellular response to amyloid-beta / mitotic spindle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cold-induced thermogenesis / amyloid-beta binding / Clathrin-mediated endocytosis / microtubule cytoskeleton / transcription by RNA polymerase II / G alpha (s) signalling events / early endosome / periplasmic space / electron transfer activity / positive regulation of MAPK cascade / lysosome / cell surface receptor signaling pathway / signaling receptor complex / endosome membrane / endosome / apical plasma membrane / Ub-specific processing proteases / cilium / ciliary basal body / iron ion binding / heme binding / protein-containing complex binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / membrane / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Beta 2 adrenoceptor / Adrenoceptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
Beta-2 adrenergic receptor / Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 29, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36342.png

Downloads & links

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Map

FileDownload / File: emd_36342.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.522
Minimum - Maximum-4.8154283 - 6.930166
Average (Standard dev.)0.00004163945 (±0.11308034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36342_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36342_half_map_2.map
Projections & Slices
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Sample components

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

EntireName: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist
Components
  • Complex: Cryo-EM structure of the beta2AR-mBRIL/1b3 Fab/Glue complex with a partial agonist
    • Protein or peptide: Beta-2 adrenergic receptor,Soluble cytochrome b562
  • Ligand: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide

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

SupramoleculeName: 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)

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Macromolecule #1: Beta-2 adrenergic receptor,Soluble cytochrome b562

MacromoleculeName: 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, Soluble cytochrome b562, Beta-2 adrenergic receptor

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Macromolecule #2: ~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino...

MacromoleculeName: ~{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 weightTheoretical: 344.405 Da
Chemical component information

ChemComp-H98:
~{N}-[5-[(1~{R})-2-[[(2~{R})-1-(4-methoxyphenyl)propan-2-yl]amino]-1-oxidanyl-ethyl]-2-oxidanyl-phenyl]methanamide

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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
VitrificationCryogen name: NITROGEN

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 327890
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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