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- EMDB-74920: Structure of AT118-R nanobody in complex with the angiotensin II ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74920
TitleStructure of AT118-R nanobody in complex with the angiotensin II type I receptor bound to L-162,313
Map data
Sample
  • Complex: Structure of AT118-R Nanobody in Complex with the Angiotensin II Type I Receptor bound to L-162,313
    • Complex: AT118-R nanobody fused to Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
      • Protein or peptide: AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
    • Complex: BAG2 Anti-BRIL Fab
      • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
      • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: butyl [3-{4-[(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)methyl]phenyl}-5-(2-methylpropyl)thiophene-2-sulfonyl]carbamate
KeywordsGPCR / nanobody / MEMBRANE 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 / phospholipase C-activating angiotensin-activated signaling pathway / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / 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 / phospholipase C-activating angiotensin-activated signaling pathway / bradykinin receptor binding / renin-angiotensin regulation of aldosterone production / 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 / regulation of vasoconstriction / Rho protein signal transduction / kidney development / blood vessel diameter maintenance / angiotensin-activated signaling pathway / Peptide ligand-binding receptors / calcium-mediated signaling / cell chemotaxis / electron transport chain / 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 / Clathrin-mediated endocytosis / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / G alpha (q) signalling events / electron transfer activity / periplasmic space / iron ion binding / inflammatory response / G protein-coupled receptor signaling pathway / protein heterodimerization activity / heme binding / symbiont entry into host cell / membrane / plasma membrane
Similarity search - Function
Angiotensin II receptor type 1 / Angiotensin II receptor 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 ...Angiotensin II receptor type 1 / Angiotensin II receptor 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
Soluble cytochrome b562 / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSkiba MA / Kruse AC
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)K99HD110612 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA260415 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R21HD101596 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL176532 United States
CitationJournal: To Be Published
Title: Activation of the angiotensin II type I receptor by a non-peptide agonist
Authors: Skiba MA / Liu J / Shen P / Kim J / Wren E / Gilman MSA / Staus D / McMahon C / Smith JS / Lefkowitz RJ / Kahne D / Wingler LM / Kruse AC
History
DepositionJan 3, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74920.png

Downloads & links

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Map

FileDownload / File: emd_74920.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.7378838 - 2.350763
Average (Standard dev.)0.00030497953 (±0.028871395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 292.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: global map

Fileemd_74920_additional_1.map
Annotationglobal map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: global half map

Fileemd_74920_additional_2.map
Annotationglobal half map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Additional map: global half map

Fileemd_74920_additional_3.map
Annotationglobal half map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: local half map

Fileemd_74920_half_map_1.map
Annotationlocal half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: local half map

Fileemd_74920_half_map_2.map
Annotationlocal half map
Projections & Slices
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Sample components

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Entire : Structure of AT118-R Nanobody in Complex with the Angiotensin II ...

EntireName: Structure of AT118-R Nanobody in Complex with the Angiotensin II Type I Receptor bound to L-162,313
Components
  • Complex: Structure of AT118-R Nanobody in Complex with the Angiotensin II Type I Receptor bound to L-162,313
    • Complex: AT118-R nanobody fused to Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
      • Protein or peptide: AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
    • Complex: BAG2 Anti-BRIL Fab
      • Protein or peptide: BAG2 Anti-BRIL Fab Heavy Chain
      • Protein or peptide: BAG2 Anti-BRIL Fab Light Chain
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: butyl [3-{4-[(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)methyl]phenyl}-5-(2-methylpropyl)thiophene-2-sulfonyl]carbamate

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Supramolecule #1: Structure of AT118-R Nanobody in Complex with the Angiotensin II ...

SupramoleculeName: Structure of AT118-R Nanobody in Complex with the Angiotensin II Type I Receptor bound to L-162,313
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: AT118-R nanobody fused to Type-1 angiotensin II receptor with Sol...

SupramoleculeName: AT118-R nanobody fused to Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: BAG2 Anti-BRIL Fab

SupramoleculeName: BAG2 Anti-BRIL Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cyto...

MacromoleculeName: AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.389816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGGG LVQAGGSLRL SCAASGYIYR KYRMGWYRQA PGKEREFVAG INGGSSTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAAYR IVRGLLVYWG QGTQVTVSSL EGGSGEDQVD PRLIDGKILN SSTEDGIKRI QDDCPKAGRH N YIFVMIPT ...String:
QVQLQESGGG LVQAGGSLRL SCAASGYIYR KYRMGWYRQA PGKEREFVAG INGGSSTNYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCAAYR IVRGLLVYWG QGTQVTVSSL EGGSGEDQVD PRLIDGKILN SSTEDGIKRI QDDCPKAGRH N YIFVMIPT LYSIIFVVGI FGNSLVVIVI YFYMKLKTVA SVFLLNLALA DLCFLLTLPL WAVYTAMEYR WPFGNYLCKI AS ASVSFNL YASVFLLTCL SIDRYLAIVH PMKSRLRRTM LVAKVTCIII WLLAGLASLP AIIHRNVFFI ENTNITVCAF HYE SQNSTL PIGLGLTKNI LGFLFPFLII LTSYTLIWKA LKKAYDLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDA QKATP PKLEDKSPDS PEMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LERARSTLDK LNDDI FKII MAIVLFFFFS WIPHQIFTFL DVLIQLGIIR DCRIADIVDT AMPITICIAY FNNCLNPLFY GFLGKKFKRY FLQLLK YGG SSLEVLFQGP TETSQVAPA

UniProtKB: Type-1 angiotensin II receptor, Soluble cytochrome b562, Type-1 angiotensin II receptor

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Macromolecule #2: BAG2 Anti-BRIL Fab Heavy Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 24.539314 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVVDFSLHWV RQAPGKGLEW VAYISSSSGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARWGYWPGEP WWKAFDYWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCD

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Macromolecule #3: BAG2 Anti-BRIL Fab Light Chain

MacromoleculeName: BAG2 Anti-BRIL Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.541164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYLYYSLVTF GQGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #5: butyl [3-{4-[(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)...

MacromoleculeName: butyl [3-{4-[(2-ethyl-5,7-dimethyl-3H-imidazo[4,5-b]pyridin-3-yl)methyl]phenyl}-5-(2-methylpropyl)thiophene-2-sulfonyl]carbamate
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1C42
Molecular weightTheoretical: 582.777 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
SoftwareName: SerialEM (ver. 4.0.5)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 6182 / Average electron dose: 63.88 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Particle selectionNumber selected: 3596857
CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab Initio Model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 464275
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)

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Image processing #2

Image processing ID2
Particle selectionNumber selected: 1830526
CTF correctionSoftware - Name: cryoSPARC (ver. 3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab Initio Model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 464275
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)

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