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- EMDB-72097: Structure of angiotensin II type 1 receptor bound to a b-arrestin... -

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Basic information

Entry
Database: EMDB / ID: EMD-72097
TitleStructure of angiotensin II type 1 receptor bound to a b-arrestin biased allosteric modulator stabilized by a synthetic nanobody
Map dataPrimary map for the AT1R-AT110i1 complex.
Sample
  • Complex: AT1R and Nanobody AT110i1 complex occupied by the orthosteric ligand TRV023 and the allosteric modulator Cmpd-23
    • Complex: AT1R
      • Protein or peptide: Type-1 angiotensin II receptor
    • Complex: TRV023
      • Protein or peptide: TRV023
    • Complex: AT110i1
      • Protein or peptide: Nanobody NB.AT110i1
  • Ligand: CHOLESTEROL
  • Ligand: (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
KeywordsAngiotensin II Type 1 Receptor / AT1R / G protein-coupled receptor / GPCR / SIGNALING PROTEIN
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
Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLiu S / Peng X / Pakharukova N / Ahn S / Lefkowitz RJ
Funding support United States, 2 items
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 EJ / Lucero EY / Vestergaard M / Wang J / Jyothidasan A / Angus L / Qu C / Olsen E / Mazis G / Madsen JK / Suomivuori C-M / Kim J / Pakharukova N / Rahman R ...Authors: Liu S / Xiao P / Elgeti M / Fine EJ / Lucero EY / Vestergaard M / Wang J / Jyothidasan A / Angus L / Qu C / Olsen E / Mazis G / Madsen JK / Suomivuori C-M / Kim J / Pakharukova N / Rahman R / Kereliuk SM / Koch W / Strachan RT / Staus DP / Masoudi A / Hubbell WL / Kahsai AW / Dror RO / Rockman HA / Sun J-P / Ahn S / Lefkowitz RJ
History
DepositionAug 12, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72097.png

Downloads & links

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Map

FileDownload / File: emd_72097.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map for the AT1R-AT110i1 complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 Å		1.1 Å/pix.
x 336 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.5501831 - 1.3519881
Average (Standard dev.)-0.00049003726 (±0.016169608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 369.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_72097_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_72097_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AT1R and Nanobody AT110i1 complex occupied by the orthosteric lig...

EntireName: AT1R and Nanobody AT110i1 complex occupied by the orthosteric ligand TRV023 and the allosteric modulator Cmpd-23
Components
  • Complex: AT1R and Nanobody AT110i1 complex occupied by the orthosteric ligand TRV023 and the allosteric modulator Cmpd-23
    • Complex: AT1R
      • Protein or peptide: Type-1 angiotensin II receptor
    • Complex: TRV023
      • Protein or peptide: TRV023
    • Complex: AT110i1
      • Protein or peptide: Nanobody NB.AT110i1
  • Ligand: CHOLESTEROL
  • Ligand: (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

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Supramolecule #1: AT1R and Nanobody AT110i1 complex occupied by the orthosteric lig...

SupramoleculeName: AT1R and Nanobody AT110i1 complex occupied by the orthosteric ligand TRV023 and the allosteric modulator Cmpd-23
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: AT1R

SupramoleculeName: AT1R / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: Angiotensin II type 1 receptor, recombinantly expressed from Expi293 cells, solubilized in detergent
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: TRV023

SupramoleculeName: TRV023 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Synthetic peptide ligand TRV023 occupying the receptor orthosteric site
Source (natural)Organism: synthetic construct (others)

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Supramolecule #4: AT110i1

SupramoleculeName: AT110i1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Details: Nanobody binding to the AT1R and stabilizing an active state of the receptor.
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Type-1 angiotensin II receptor

MacromoleculeName: Type-1 angiotensin II receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.968691 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKIL NSSTEDGIKR IQDDCPKAGR HNYIFVMIPT LYSIIFVVGI FGNSLVVIVI YFYMKLKTVA SVFLLNLALA DLCFLLTLP LWAVYTAMEY RWPFGNYLCK IASASVSFNL YASVFLLTCL SIDRYLAIVH PMKSRLRRTM LVAKVTCIII W LLAGLASL ...String:
DYKDDDDKIL NSSTEDGIKR IQDDCPKAGR HNYIFVMIPT LYSIIFVVGI FGNSLVVIVI YFYMKLKTVA SVFLLNLALA DLCFLLTLP LWAVYTAMEY RWPFGNYLCK IASASVSFNL YASVFLLTCL SIDRYLAIVH PMKSRLRRTM LVAKVTCIII W LLAGLASL PAIIHRNVFF IENTNITVCA FHYESQNSTL PIGLGLTKNI LGFLFPFLII LTSYTLIWKA LKKAYEIQKN KP RNDDIFK IIMAIVLFFF FSWIPHQIFT FLDVLIQLGI IRDCRIADIV DTAMPITICI AYFNNCLNPL FYGFLGKKFK RYF LQLLKY IPPKAKSHSN LSTKMSTLSY RPSDNVSSST KKPAPCFEVE

UniProtKB: Type-1 angiotensin II receptor

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Macromolecule #2: TRV023

MacromoleculeName: TRV023 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 944.111 Da
SequenceString:
(SAR)RVYKHPA

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Macromolecule #3: Nanobody NB.AT110i1

MacromoleculeName: Nanobody NB.AT110i1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.783131 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGNIFD VDIMGWYRQA PGKERELVAS ITDGGSTDYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAAVA YPDIPTYFDY DSDNFYWGQG TQVTVSSLEH HHHHH

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: (7P)-N-[(1R)-3-amino-1-(6-methoxypyridin-3-yl)-3-oxopropyl]-7-(3-...

MacromoleculeName: (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
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1CNF
Molecular weightTheoretical: 692.13 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 56.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 907280
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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