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- PDB-9zxd: Structure of AT118-R nanobody in complex with the angiotensin II ... -

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Basic information

Entry
Database: PDB / ID: 9zxd
TitleStructure of AT118-R nanobody in complex with the angiotensin II type I receptor bound to L-162,313
Components
  • AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
  • BAG2 Anti-BRIL Fab Heavy Chain
  • BAG2 Anti-BRIL Fab Light Chain
KeywordsMEMBRANE PROTEIN / GPCR / nanobody
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
: / CHOLESTEROL HEMISUCCINATE / Soluble cytochrome b562 / Type-1 angiotensin II receptor
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSkiba, M.A. / Kruse, A.C.
Funding support United States, 4items
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, M.A. / Liu, J. / Shen, P. / Kim, J. / Wren, E. / Gilman, M.S.A. / Staus, D. / McMahon, C. / Smith, J.S. / Lefkowitz, R.J. / Kahne, D. / Wingler, L.M. / Kruse, A.C.
History
DepositionJan 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion
C: BAG2 Anti-BRIL Fab Heavy Chain
D: BAG2 Anti-BRIL Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5405
Polymers113,4703
Non-polymers1,0702
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein AT118-R nanobody,Type-1 angiotensin II receptor with Soluble cytochrome b562 insertion


Mass: 65389.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B, cybC / Production host: Homo sapiens (human) / References: UniProt: P30556, UniProt: P0ABE7
#2: Antibody BAG2 Anti-BRIL Fab Heavy Chain


Mass: 24539.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#3: Antibody BAG2 Anti-BRIL Fab Light Chain


Mass: 23541.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#5: Chemical ChemComp-A1C42 / 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 / L-162,313


Mass: 582.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H38N4O4S2 / 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-IDSource
1Structure of AT118-R Nanobody in Complex with the Angiotensin II Type I Receptor bound to L-162,313COMPLEX#1-#30MULTIPLE SOURCES
2AT118-R nanobody fused to Type-1 angiotensin II receptor with Soluble cytochrome b562 insertionCOMPLEX#11RECOMBINANT
3BAG2 Anti-BRIL FabCOMPLEX#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
32Escherichia coli (E. coli)562
42synthetic construct (others)32630
53synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606Expi293
33Homo sapiens (human)9606
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 63.88 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 6182
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1cryoSPARC3particle selection1
2PHENIX1.21.1_5286model refinement
3SerialEM4.0.5image acquisition1
5cryoSPARC3CTF correction1
10cryoSPARC3initial Euler assignment1
11cryoSPARC3final Euler assignment1
13cryoSPARC33D reconstruction1
14cryoSPARC3particle selection2
15cryoSPARC3CTF correction2
16cryoSPARC3initial Euler assignment2
17cryoSPARC3final Euler assignment2
19cryoSPARC33D reconstruction2
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
IDImage processing-IDNum. of particles selected
113596857
221830526
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.2FSC 0.143 CUT-OFF46427519ZXDPOINT
23.2FSC 0.143 CUT-OFF46427519ZXDPOINT
33.2FSC 0.143 CUT-OFF46427529ZXDPOINT
43.2FSC 0.143 CUT-OFF46427529ZXDPOINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0045883
ELECTRON MICROSCOPYf_angle_d0.5648000
ELECTRON MICROSCOPYf_dihedral_angle_d7.676889
ELECTRON MICROSCOPYf_chiral_restr0.04897
ELECTRON MICROSCOPYf_plane_restr0.004985

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