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- PDB-9q0f: Structure of angiotensin II type 1 receptor bound to a b-arrestin... -

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Basic information

Entry
Database: PDB / ID: 9q0f
TitleStructure of angiotensin II type 1 receptor bound to a b-arrestin biased allosteric modulator stabilized by a synthetic nanobody
Components
  • Nanobody NB.AT110i1
  • TRV023
  • Type-1 angiotensin II receptor
KeywordsSIGNALING PROTEIN / Angiotensin II Type 1 Receptor / AT1R / G protein-coupled receptor / GPCR
Function / homology
Function and homology information


angiotensin type I receptor activity / angiotensin type II receptor activity / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / renin-angiotensin regulation of aldosterone production / phospholipase C-activating angiotensin-activated signaling pathway / bradykinin receptor binding / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cholesterol metabolic process / low-density lipoprotein particle remodeling ...angiotensin type I receptor activity / angiotensin type II receptor activity / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / renin-angiotensin regulation of aldosterone production / phospholipase C-activating angiotensin-activated signaling pathway / bradykinin receptor binding / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of cholesterol metabolic process / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / regulation of systemic arterial blood pressure by renin-angiotensin / Rho protein signal transduction / regulation of vasoconstriction / kidney development / blood vessel diameter maintenance / angiotensin-activated signaling pathway / Peptide ligand-binding receptors / calcium-mediated signaling / cell chemotaxis / regulation of cell growth / regulation of blood pressure / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of cell population proliferation / Cargo recognition for clathrin-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / Clathrin-mediated endocytosis / regulation of inflammatory response / G alpha (q) signalling events / inflammatory response / G protein-coupled receptor signaling pathway / protein heterodimerization activity / symbiont entry into host cell / membrane / plasma membrane
Similarity search - Function
Angiotensin II receptor type 1 / Angiotensin II receptor family / : / 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
: / CHOLESTEROL / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu, S. / Peng, X. / Pakharukova, N. / Ahn, S. / Lefkowitz, R.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 HL16037 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Conformational Basis of Functionally Selective Allosteric Modulation of the Angiotensin II type 1 Receptor by Small Molecules
Authors: Liu, S. / Xiao, P. / Elgeti, M. / Fine, E.J. / Lucero, E.Y. / Vestergaard, M. / Wang, J. / Jyothidasan, A. / Angus, L. / Qu, C. / Olsen, E. / Mazis, G. / Madsen, J.K. / Suomivuori, C.-M. / ...Authors: Liu, S. / Xiao, P. / Elgeti, M. / Fine, E.J. / Lucero, E.Y. / Vestergaard, M. / Wang, J. / Jyothidasan, A. / Angus, L. / Qu, C. / Olsen, E. / Mazis, G. / Madsen, J.K. / Suomivuori, C.-M. / Kim, J. / Pakharukova, N. / Rahman, R. / Kereliuk, S.M. / Koch, W. / Strachan, R.T. / Staus, D.P. / Masoudi, A. / Hubbell, W.L. / Kahsai, A.W. / Dror, R.O. / Rockman, H.A. / Sun, J.-P. / Ahn, S. / Lefkowitz, R.J.
History
DepositionAug 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type-1 angiotensin II receptor
B: TRV023
D: Nanobody NB.AT110i1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1616
Polymers57,6963
Non-polymers1,4653
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Type-1 angiotensin II receptor / AT1AR / AT1BR / Angiotensin II type-1 receptor / AT1 receptor


Mass: 41968.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B / Plasmid: pcDNA-Zeo-tetO / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P30556
#2: Protein/peptide TRV023


Mass: 944.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Antibody Nanobody NB.AT110i1


Mass: 14783.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#4: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical ChemComp-A1CNF / (7P)-N-[(1R)-3-amino-1-(6-methoxypyridin-3-yl)-3-oxopropyl]-7-(3-chlorophenyl)-5,6-dimethyl-4-(3-{[2-(trifluoromethyl)phenyl]methyl}azetidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine-2-carboxamide


Mass: 692.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H33ClF3N7O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails (eV)
1AT1R and Nanobody AT110i1 complex occupied by the orthosteric ligand TRV023 and the allosteric modulator Cmpd-23COMPLEX#1-#30MULTIPLE SOURCES
2AT1RCOMPLEX#11RECOMBINANTAngiotensin II type 1 receptor, recombinantly expressed from Expi293 cells, solubilized in detergent
3TRV023COMPLEX#21MULTIPLE SOURCESSynthetic peptide ligand TRV023 occupying the receptor orthosteric site
4AT110i1COMPLEX#31RECOMBINANTNanobody binding to the AT1R and stabilizing an active state of the receptor.
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23synthetic construct (others)32630
34synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
12Homo sapiens (human)9606Expi293pcDNA-Zeo-tetO
24Escherichia coli BL21(DE3) (bacteria)469008BL21
Buffer solutionpH: 7.4
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 907280 / Symmetry type: POINT
RefinementHighest resolution: 3.02 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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