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- PDB-1yk0: structure of natriuretic peptide receptor-C complexed with atrial... -

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Basic information

Entry
Database: PDB / ID: 1yk0
Titlestructure of natriuretic peptide receptor-C complexed with atrial natriuretic peptide
Components(Atrial natriuretic ...) x 2
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / HORMONE-RECEPTOR COMPLEX / NATRIURETIC PEPTIDE RECEPTOR / ALLOSTERIC ACTIVATION / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / osteoclast proliferation / receptor guanylyl cyclase signaling pathway / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors ...positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / osteoclast proliferation / receptor guanylyl cyclase signaling pathway / neuropeptide receptor binding / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / cGMP biosynthetic process / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / hormone binding / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / sodium ion export across plasma membrane / positive regulation of urine volume / negative regulation of JUN kinase activity / regulation of osteoblast proliferation / neuropeptide hormone activity / G protein-coupled peptide receptor activity / negative regulation of systemic arterial blood pressure / cardiac muscle hypertrophy in response to stress / hormone receptor binding / aortic valve morphogenesis / negative regulation of cold-induced thermogenesis / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / chloride ion binding / positive regulation of heart rate / cGMP-mediated signaling / peptide hormone binding / neuropeptide signaling pathway / blood vessel remodeling / positive regulation of cardiac muscle contraction / response to muscle stretch / cell projection / skeletal system development / positive regulation of nitric-oxide synthase activity / female pregnancy / response to ischemia / peptide binding / hormone activity / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / angiogenesis / Amyloid fiber formation / signaling receptor binding / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / extracellular region / 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 / Response regulator / Receptor, ligand binding region ...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 / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Natriuretic peptides A / Atrial natriuretic peptide receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHe, X. / Garcia, K.C.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural determinants of natriuretic peptide receptor specificity and degeneracy.
Authors: He, X.L. / Dukkipati, A. / Garcia, K.C.
History
DepositionJan 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Atrial natriuretic peptide clearance receptor
B: Atrial natriuretic peptide clearance receptor
E: Atrial natriuretic factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,1349
Polymers107,9753
Non-polymers1,1596
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.866, 135.468, 137.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models2

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Components

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

#1: Protein Atrial natriuretic peptide clearance receptor / ANP-C / ANPRC / NPR-C / Atrial natriuretic peptide C-type receptor


Mass: 52904.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPR3, ANPRC / Plasmid: PRMHA3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P17342
#2: Protein/peptide Atrial natriuretic factor


Mass: 2165.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P01160

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Sugars , 2 types, 4 molecules

#3: 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.: 1 / Source method: isolated from a natural 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
#4: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: isolated from a natural source / 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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Non-polymers , 2 types, 322 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JDP

1jdp


Resolution: 2.4→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Rfactor% reflectionSelection details
Rfree0.284 -random
Rwork0.24 --
all0.242 --
obs0.242 98.6 %-
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 72 320 6763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.4→2.49 Å /
Rfactor% reflection
Rfree0.389 -
Rwork0.394 -
obs-98.6 %

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