6DO1

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

PDB DOI: https://doi.org/10.2210/pdb6DO1/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Escherichia coli, synthetic construct
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2018-06-08 Released: 2019-01-30
Deposition Author(s): Wingler, L.M., McMahon, C., Staus, D.P., Lefkowitz, R.J., Kruse, A.C.
Funding Organization(s): National Institutes of Health/Office of the Director, National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), Other private, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.359
R-Value Work: 0.304
R-Value Observed: 0.308

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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

PubMed: 30639100 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2018.12.006
Primary Citation of Related Structures:
6DO1

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 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.

Macromolecule Content

Total Structure Weight: 156.22 kDa
Atom Count: 7,930
Modelled Residue Count: 1,008
Deposited Residue Count: 1,370
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type-1 angiotensin II receptor,Soluble cytochrome b562 BRIL fusion protein	A, B	425	Homo sapiens, Escherichia coli	Mutation(s): 1 Gene Names: AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B, cybC Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P30556 (Homo sapiens) Explore P30556 Go to UniProtKB: P30556
PHAROS: P30556 GTEx: ENSG00000144891
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P30556
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody Nb.AT110i1	C, D, E, F	126	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-like peptide S1I8	G, H	8	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLC Query on OLC Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	M [auth A], N [auth A], R [auth B], S [auth B], T [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B]	I [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain P [auth B] Focus chain Q [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SAR Query on SAR	G, H	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.359
R-Value Work: 0.304
R-Value Observed: 0.308
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.682	α = 90
b = 227.796	β = 90
c = 41.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
JBluIce-EPICS	data collection
Coot	model building
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/Office of the Director	United States	5DP5OD021345
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	R01HL16037
Other private	United States	The Vallee Foundation
Other private	United States	The Smith Family Foundation
Other private	United States	Mandel Center for Hypertension and Atherosclerosis
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2019-02-06
Changes: Data collection, Database references
Version 1.2: 2019-11-20
Changes: Author supporting evidence
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary