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 
- 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 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(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 | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nanobody Nb.AT110i1 | 126 | synthetic construct | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Angiotensin-like peptide S1I8 | 8 | synthetic construct | Mutation(s): 0  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
OLC Query on OLC | 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 | |||
NAG Query on NAG | I [auth A], O [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
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 Name | Purpose |
---|---|
PHENIX | refinement |
JBluIce-EPICS | data collection |
Coot | model building |
PHASER | phasing |
XDS | data reduction |
Aimless | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-01-30  Deposition Author(s): Wingler, L.M., McMahon, C., Staus, D.P., Lefkowitz, R.J., Kruse, A.C.
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