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Yorodumi- PDB-8tg9: Complex of NPR1 ectodomain with ANP plus an allosteric activating... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tg9 | ||||||
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Title | Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Atrial natriuretic peptide / antibody / activator / pulmonary hypertension | ||||||
Function / homology | Function and homology information positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / neuropeptide receptor binding / positive regulation of renal sodium excretion / regulation of high voltage-gated calcium channel activity ...positive regulation of delayed rectifier potassium channel activity / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / body fluid secretion / peptide receptor activity / neuropeptide receptor binding / positive regulation of renal sodium excretion / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / hormone binding / regulation of vascular permeability / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / negative regulation of JUN kinase activity / sodium ion export across plasma membrane / positive regulation of urine volume / neuropeptide hormone activity / cardiac muscle hypertrophy in response to stress / G protein-coupled peptide receptor activity / hormone receptor binding / negative regulation of systemic arterial blood pressure / adenylate cyclase activity / aortic valve morphogenesis / cGMP-mediated signaling / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / response to muscle stretch / negative regulation of angiogenesis / blood vessel diameter maintenance / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / hormone activity / negative regulation of cell growth / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / receptor complex / cell surface receptor signaling pathway / protein kinase activity / Amyloid fiber formation / signaling receptor binding / GTP binding / protein-containing complex / extracellular space / extracellular region / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å | ||||||
Authors | Franklin, M.C. / Romero Hernandez, A. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381 Authors: Franklin, M.C. / Romero Hernandez, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tg9.cif.gz | 315.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tg9.ent.gz | 250.5 KB | Display | PDB format |
PDBx/mmJSON format | 8tg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tg9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8tg9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8tg9_validation.xml.gz | 56.2 KB | Display | |
Data in CIF | 8tg9_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/8tg9 ftp://data.pdbj.org/pub/pdb/validation_reports/tg/8tg9 | HTTPS FTP |
-Related structure data
Related structure data | 41233MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Atrial natriuretic ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 52263.723 Da / Num. of mol.: 2 / Fragment: ectodomain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NPR1, ANPRA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16066, guanylate cyclase #2: Protein/peptide | | Mass: 3087.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01160 |
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-Antibody , 2 types, 4 molecules HELF
#3: Antibody | Mass: 24818.770 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Velocimmune mouse / Production host: Cricetulus griseus (Chinese hamster) #4: Antibody | Mass: 23323.898 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Velocimmune mouse / Production host: Cricetulus griseus (Chinese hamster) |
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-Sugars , 4 types, 6 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Cricetulus griseus (Chinese hamster) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1299989 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 682951 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.81 Å2 | ||||||||||||||||||||||||
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