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- Structure Factors (CIF)
- Structure Factors (CIF - gz)
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- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
4YAY | pdb_00004yay
XFEL structure of human Angiotensin Receptor
- PDB DOI: https://doi.org/10.2210/pdb4YAY/pdb
- Classification: MEMBRANE PROTEIN
- Organism(s): Escherichia coli, Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes
- Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc
- Deposited: 2015-02-18 Released: 2015-04-22
- Deposition Author(s): Zhang, H., Unal, H., Gati, C., Han, G.W., Zatsepin, N.A., James, D., Wang, D., Nelson, G., Weierstall, U., Messerschmidt, M., Williams, G.J., Boutet, S., Yefanov, O.M., White, T.A., Liu, W., Ishchenko, A., Tirupula, K.C., Desnoyer, R., Sawaya, M.C., Xu, Q., Coe, J., Cornrad, C.E., Fromme, P., Stevens, R.C., Katritch, V., Karnik, S.S., Cherezov, V., GPCR Network (GPCR)
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.274 (Depositor), 0.316 (DCC)
- R-Value Work: 0.228 (Depositor), 0.260 (DCC)
- R-Value Observed: 0.231 (Depositor)
Starting Model: other
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Literature
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Structure of the Angiotensin receptor revealed by serial femtosecond crystallography.
Zhang, H., Unal, H., Gati, C., Han, G.W., Liu, W., Zatsepin, N.A., James, D., Wang, D., Nelson, G., Weierstall, U., Sawaya, M.R., Xu, Q., Messerschmidt, M., Williams, G.J., Boutet, S., Yefanov, O.M., White, T.A., Wang, C., Ishchenko, A., Tirupula, K.C., Desnoyer, R., Coe, J., Conrad, C.E., Fromme, P., Stevens, R.C., Katritch, V., Karnik, S.S., Cherezov, V.(2015) Cell 161: 833-844
- PubMed: 25913193 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1016/j.cell.2015.04.011
- Primary Citation Related Structures:
4YAY - PubMed Abstract:
Angiotensin II type 1 receptor (AT(1)R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT(1)R blockers (ARBs), the structural basis for AT(1)R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high-quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT(1)R in complex with its selective antagonist ZD7155 at 2.9-Å resolution. The AT(1)R-ZD7155 complex structure revealed key structural features of AT(1)R and critical interactions for ZD7155 binding. Docking simulations of the clinically used ARBs into the AT(1)R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT(1)R structure-function relationship and structure-based drug design.
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
- Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607 Hamburg, Germany.
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089 USA.
- Department of Chemistry and Biochemistry, Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
- Department of Chemistry and Biochemistry, the UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- BioXFEL Science and Technology Center, Buffalo, NY 14203, USA.
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089 USA; iHuman Institute, ShanghaiTech University, Shanghai, 201210 China.
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089 USA. Electronic address: cherezov@usc.edu.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZD7) | Predict Membrane
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZD7) | Predict Membrane
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 47.68 kDa
- Atom Count: 3,110
- Modeled Residue Count: 393
- Deposited Residue Count: 414
- Unique protein chains: 1
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Soluble cytochrome b562,Type-1 angiotensin II receptor | 414 | Escherichia coli, Homo sapiens This entity is chimeric | Mutation(s): 3 Gene Names: cybC, AGTR1, AGTR1A, AGTR1B, AT2R1, AT2R1B Membrane Entity: Yes | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P30556 GTEx: ENSG00000144891 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Groups | P0ABE7P30556 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZD7 Download:Ideal Coordinates CCD File | B [auth A] | 5,7-diethyl-1-{[2'-(1H-tetrazol-5-yl)biphenyl-4-yl]methyl}-3,4-dihydro-1,6-naphthyridin-2(1H)-one C26 H26 N6 O BFVNEYDCFJNLGN-UHFFFAOYSA-N | 👁 Image | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.274 (Depositor), 0.316 (DCC)
- R-Value Work: 0.228 (Depositor), 0.260 (DCC)
- R-Value Observed: 0.231 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.8 | α = 90 |
| b = 41 | β = 99.4 |
| c = 167.7 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| PHASER | phasing |
| CrystFEL | data scaling |
| CrystFEL | data reduction |
Entry History
& Funding InformationDeposition Data
- Released Date: 2015-04-22 Deposition Author(s): Zhang, H., Unal, H., Gati, C., Han, G.W., Zatsepin, N.A., James, D., Wang, D., Nelson, G., Weierstall, U., Messerschmidt, M., Williams, G.J., Boutet, S., Yefanov, O.M., White, T.A., Liu, W., Ishchenko, A., Tirupula, K.C., Desnoyer, R., Sawaya, M.C., Xu, Q., Coe, J., Cornrad, C.E., Fromme, P., Stevens, R.C., Katritch, V., Karnik, S.S., Cherezov, V., GPCR Network (GPCR)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | U54 GM094618 |
Revision History (Full details and data files)
- Version 1.0: 2015-04-22
Type: Initial release - Version 1.1: 2015-05-06
Changes: Structure summary - Version 1.2: 2015-05-13
Changes: Database references - Version 1.3: 2015-05-27
Changes: Database references - Version 1.4: 2017-09-06
Changes: Author supporting evidence, Derived calculations, Source and taxonomy - Version 1.5: 2017-11-22
Changes: Refinement description - Version 1.6: 2018-02-14
Changes: Data collection - Version 1.7: 2019-12-25
Changes: Author supporting evidence - Version 1.8: 2023-08-16
Changes: Data collection, Database references - Version 1.9: 2024-10-23
Changes: Refinement description, Structure summary
