+
Open data
-
Basic information
Entry | Database: PDB / ID: 7c6a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of AT2R-BRIL and SRP2070_Fab complex | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / GPCR / BRIL / Crystallization / Antibody | ||||||
Function / homology | ![]() angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / angiotensin type II receptor activity / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / : / regulation of renal sodium excretion ...angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / regulation of metanephros size / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / angiotensin type II receptor activity / regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / : / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / positive regulation of metanephric glomerulus development / regulation of extracellular matrix assembly / receptor antagonist activity / regulation of renal output by angiotensin / positive regulation of activation of Janus kinase activity / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renal system process / renin-angiotensin regulation of aldosterone production / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / C-C chemokine receptor activity / C-C chemokine binding / vasoconstriction / positive regulation of CoA-transferase activity / type 1 angiotensin receptor binding / low-density lipoprotein particle remodeling / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / exploration behavior / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of heart rate / positive regulation of cardiac muscle hypertrophy / positive regulation of phosphoprotein phosphatase activity / negative regulation of blood vessel endothelial cell migration / positive regulation of gap junction assembly / positive regulation of protein tyrosine kinase activity / regulation of vasoconstriction / regulation of cardiac conduction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / neurogenesis / cell chemotaxis / negative regulation of MAP kinase activity / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / calcium-mediated signaling / electron transport chain / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / brain development / PPARA activates gene expression / negative regulation of cell growth / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / vasodilation / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (q) signalling events / regulation of apoptotic process / neuron apoptotic process / collagen-containing extracellular matrix / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / inflammatory response / iron ion binding / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / heme binding / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Suzuki, M. / Miyagi, H. / Asada, H. / Yasunaga, M. / Suno, C. / Takahashi, Y. / Saito, J. / Iwata, S. | ||||||
![]() | ![]() Title: The discovery of a new antibody for BRIL-fused GPCR structure determination. Authors: Miyagi, H. / Asada, H. / Suzuki, M. / Takahashi, Y. / Yasunaga, M. / Suno, C. / Iwata, S. / Saito, J.I. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 339.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 277.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 475.2 KB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7c61C ![]() 4zudS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23681.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Antibody | Mass: 24240.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 48086.391 Da / Num. of mol.: 1 / Mutation: L93V, F133W, M1007W, H1102I, R1106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: AGTR2, cybC / Production host: ![]() ![]() |
#4: Protein/peptide | Mass: 970.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.05M POTASSIUM ACETATE, 0.1M MES PH6.5, 26-36% PEG300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 16, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→42.77 Å / Num. obs: 16178 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.607 / Rpim(I) all: 0.14 / Rrim(I) all: 0.623 / Net I/σ(I): 5.1 / Num. measured all: 303868 / Scaling rejects: 44 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4ZUD Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.634 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 241.42 Å2 / Biso mean: 135.009 Å2 / Biso min: 89.75 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.4→3.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|