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- PDB-8tg9: Complex of NPR1 ectodomain with ANP plus an allosteric activating... -

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Basic information

Entry
Database: PDB / ID: 8tg9
TitleComplex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Components
  • (Atrial natriuretic ...) x 2
  • (REGN5381 Fab ...) x 2
KeywordsIMMUNE 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 / body fluid secretion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / positive regulation of renal sodium excretion / neuropeptide receptor binding / 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 / body fluid secretion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / positive regulation of renal sodium excretion / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / guanylate cyclase / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / guanylate cyclase activity / 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 / positive regulation of urine volume / sodium ion export across plasma membrane / neuropeptide hormone activity / G protein-coupled peptide receptor activity / cardiac muscle hypertrophy in response to stress / hormone receptor binding / negative regulation of systemic arterial blood pressure / aortic valve morphogenesis / adenylate cyclase activity / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / negative regulation of angiogenesis / positive regulation of cardiac muscle contraction / response to muscle stretch / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / cell projection / female pregnancy / regulation of blood pressure / vasodilation / hormone activity / negative regulation of cell growth / 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
Natriuretic peptide, atrial type / : / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / : ...Natriuretic peptide, atrial type / : / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / : / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Natriuretic peptides A / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsFranklin, M.C. / Romero Hernandez, A.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Complex of NPR1 ectodomain with ANP plus an allosteric activating antibody, REGN5381
Authors: Franklin, M.C. / Romero Hernandez, A.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atrial natriuretic peptide receptor 1
B: Atrial natriuretic peptide receptor 1
C: Atrial natriuretic peptide
H: REGN5381 Fab heavy chain
L: REGN5381 Fab light chain
E: REGN5381 Fab heavy chain
F: REGN5381 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,85113
Polymers203,9007
Non-polymers2,9516
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Atrial natriuretic ... , 2 types, 3 molecules ABC

#1: Protein Atrial natriuretic peptide receptor 1 / Atrial natriuretic peptide receptor type A / ANP-A / ANPR-A / NPR-A / Guanylate cyclase A / GC-A


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 Atrial natriuretic peptide / ANP / Alpha-atrial natriuretic peptide / Alpha-hANP / Atrial natriuretic factor / ANF / CDD-ANF / ...ANP / Alpha-atrial natriuretic peptide / Alpha-hANP / Atrial natriuretic factor / ANF / CDD-ANF / CDD-ANP (99-126) / Cardionatrin / Pro atrial natriuretic factor 99-126 / proANF 99-126


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 REGN5381 Fab heavy chain


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 REGN5381 Fab light chain


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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Active complex of NPR1 ectodomain, ANP, and REGN5381 Fab
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
SpecimenConc.: 1.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1299989
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 682951 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 40.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001714039
ELECTRON MICROSCOPYf_angle_d0.454919096
ELECTRON MICROSCOPYf_chiral_restr0.03932126
ELECTRON MICROSCOPYf_plane_restr0.00352450
ELECTRON MICROSCOPYf_dihedral_angle_d3.1872019

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