6DO1

Structure of nanobody-stabilized angiotensin II type 1 receptor bound to S1I8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.304 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distinctive Activation Mechanism for Angiotensin Receptor Revealed by a Synthetic Nanobody.

Wingler, L.M.McMahon, C.Staus, D.P.Lefkowitz, R.J.Kruse, A.C.

(2019) Cell 176: 479-490.e12

  • DOI: 10.1016/j.cell.2018.12.006

  • PubMed Abstract: 
  • The angiotensin II (AngII) type 1 receptor (AT1R) is a critical regulator of cardiovascular and renal function and is an important model for studies of G-protein-coupled receptor (GPCR) signaling. By stabilizing the receptor with a single-domain anti ...

    The angiotensin II (AngII) type 1 receptor (AT1R) is a critical regulator of cardiovascular and renal function and is an important model for studies of G-protein-coupled receptor (GPCR) signaling. By stabilizing the receptor with a single-domain antibody fragment ("nanobody") discovered using a synthetic yeast-displayed library, we determined the crystal structure of active-state human AT1R bound to an AngII analog with partial agonist activity. The nanobody binds to the receptor's intracellular transducer pocket, stabilizing the large conformational changes characteristic of activated GPCRs. The peptide engages the AT1R through an extensive interface spanning from the receptor core to its extracellular face and N terminus, remodeling the ligand-binding cavity. Remarkably, the mechanism used to propagate conformational changes through the receptor diverges from other GPCRs at several key sites, highlighting the diversity of allosteric mechanisms among GPCRs. Our structure provides insight into how AngII and its analogs stimulate full or biased signaling, respectively.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Howard Hughes Medical Institute and Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA. Electronic address: lefko001@receptor-biol.duke.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: andrew_kruse@hms.harvard.edu.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein
A, B
425Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 1 
Gene Names: cybC, AGTR1 (AGTR1A, AGTR1B, AT2R1, AT2R1B)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
Angiotensin type II receptor in complex with compound 1 (monoclinic xtals)
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P30556 (Homo sapiens)
Go to Gene View: AGTR1
Go to UniProtKB:  P30556
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody Nb.AT110i1
C, D, E, F
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-like peptide S1I8
G, H
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SAR
Query on SAR
G, H
PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.901 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.304 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.682α = 90.00
b = 227.796β = 90.00
c = 41.500γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
XDSdata reduction
PHENIXrefinement
JBluIce-EPICSdata collection
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited States5DP5OD021345
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited StatesR01HL16037
Other privateUnited StatesThe Vallee Foundation
Other privateUnited StatesThe Smith Family Foundation
Other privateUnited StatesMandel Center for Hypertension and Atherosclerosis
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references