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- PDB-7brj: Atrial Natriuretic Peptide Receptor complexed with deletion mutan... -

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Basic information

Entry
Database: PDB / ID: 7brj
TitleAtrial Natriuretic Peptide Receptor complexed with deletion mutant of human Atrial Natriuretic Peptide[7-28]
Components
  • Atrial natriuretic peptide receptor 1
  • Urodilatin
KeywordsMEMBRANE PROTEIN / RECEPTOR-HORMONE COMPLEX / NATRIURETIC PEPTIDE / NATRIURETIC PEPTIDE RECEPTOR / GUANYLYL-CYCLASE-COUPLED RECEPTOR / SIGNAL TRANSMISSION / ROTATION MECHANISM / SIGNALING PROTEIN
Function / homology
Function and homology information


ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / guanylate cyclase / regulation of high voltage-gated calcium channel activity ...ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / neuropeptide receptor binding / guanylate cyclase / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / guanylate cyclase activity / 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 / negative regulation of JUN kinase activity / neuropeptide hormone activity / negative regulation of systemic arterial blood pressure / cardiac muscle hypertrophy in response to stress / adenylate cyclase activity / hormone receptor binding / aortic valve morphogenesis / 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 / positive regulation of cardiac muscle contraction / response to muscle stretch / blood vessel diameter maintenance / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / hormone activity / regulation of blood pressure / vasodilation / protein folding / perikaryon / collagen-containing extracellular matrix / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / 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 / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOgawa, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22570110 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101080, JP18am0101080 and JP19am0101080 Japan
CitationJournal: To Be Published
Title: Structural insight into hormone-recognition and transmembrane signaling by the atrial natriuretic peptide receptor
Authors: Ogawa, H.
History
DepositionMar 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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 receptor 1
B: Atrial natriuretic peptide receptor 1
L: Urodilatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,0109
Polymers99,2683
Non-polymers2,7416
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-15 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.793, 99.793, 260.397
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABL

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


Mass: 48434.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Npr1 / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P18910, guanylate cyclase
#2: Protein/peptide Urodilatin / URO / CDD 95-126 / CDD-ANP (95-126) / Pro atrial natriuretic peptide 95-126 / proANP 95-126


Mass: 2398.727 Da / Num. of mol.: 1 / Mutation: deletion of residues 1-6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01160

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Sugars , 2 types, 4 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 146 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.77 Å3/Da / Density % sol: 67.38 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium malonate, MES / PH range: 6.3 - 6.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 39908 / % possible obs: 99.3 % / Redundancy: 10.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.031 / Net I/σ(I): 23.5
Reflection shellResolution: 2.7→2.78 Å / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3316 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000716.1data reduction
HKL-2000716.1data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DP4

1dp4


Resolution: 2.7→43.258 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 27.14
RfactorNum. reflection% reflection
Rfree0.2335 1219 3.06 %
Rwork0.1927 --
obs0.194 39898 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→43.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6864 0 180 144 7188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067470
X-RAY DIFFRACTIONf_angle_d0.77910170
X-RAY DIFFRACTIONf_dihedral_angle_d13.2654418
X-RAY DIFFRACTIONf_chiral_restr0.0461126
X-RAY DIFFRACTIONf_plane_restr0.0051312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80810.37751420.31574273X-RAY DIFFRACTION100
2.8081-2.93590.32361270.28654363X-RAY DIFFRACTION100
2.9359-3.09060.29221320.26294281X-RAY DIFFRACTION100
3.0906-3.28420.26131520.24144260X-RAY DIFFRACTION100
3.2842-3.53770.22971130.2134327X-RAY DIFFRACTION99
3.5377-3.89350.24351150.17374283X-RAY DIFFRACTION99
3.8935-4.45640.21671340.15534311X-RAY DIFFRACTION99
4.4564-5.61260.19921530.15794319X-RAY DIFFRACTION100
5.6126-43.2580.20871510.17784262X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.568-0.4934-0.51033.9699-1.84652.4235-0.22760.129-0.2318-0.2815-0.2108-1.2859-0.2360.87210.42470.8808-0.18970.09350.65510.29740.918445.871312.0046-12.5883
28.03471.7180.32463.348-0.46782.29580.0325-0.39340.40210.3694-0.1662-0.0299-0.5767-0.04750.10210.8249-0.004-0.00110.27230.11980.446525.822312.706-4.3203
35.09012.7533-0.55015.46110.91585.5529-0.48870.83541.0637-0.87820.43770.8863-0.3225-0.7528-0.14440.74520.0549-0.13770.55550.23250.69799.38038.205-19.0265
43.36982.4355-0.71554.3604-0.83651.9804-0.19440.43770.7577-0.3380.1560.4631-0.8482-0.150.06311.11710.0007-0.03010.47610.27660.811825.301722.6458-15.9579
53.6239-1.6870.53255.989-2.06992.4649-0.1178-0.11020.60560.3161-0.3423-1.55290.16690.88640.3780.83110.1782-0.10.63740.31350.938245.8742-11.999612.9472
67.3705-1.6824-0.48634.1931-0.39672.64690.05930.2608-0.1768-0.4599-0.15370.01170.5888-0.07930.13470.85680.00870.00540.26780.14440.461925.8335-12.71424.67
74.7766-2.54090.34196.01030.78765.5271-0.5395-0.8375-1.10780.84870.46150.96650.3512-0.7406-0.10010.7624-0.05730.14630.52560.21740.65069.3861-8.214419.3783
83.7391-1.82380.71594.7339-1.05911.9003-0.1951-0.4264-0.69610.36910.1660.44270.8248-0.15680.0661.11610.01270.04560.4480.27120.777425.3053-22.658116.3082
90.8871-2.6562-1.69358.09434.79053.22250.31580.29710.1165-0.97020.2669-1.2765-0.70320.28950.67421.21730.0081-0.0480.59870.15480.327925.1204-1.56860.1545
100.11310.17010.13120.68260.45680.35440.0588-0.50360.0440.0373-0.39880.00580.4447-1.103-0.3041.83170.06620.58420.86160.31-0.315215.63954.33184.2982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 178 )
3X-RAY DIFFRACTION3chain 'A' and (resid 179 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 426 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 76 )
6X-RAY DIFFRACTION6chain 'B' and (resid 77 through 178 )
7X-RAY DIFFRACTION7chain 'B' and (resid 179 through 266 )
8X-RAY DIFFRACTION8chain 'B' and (resid 267 through 426 )
9X-RAY DIFFRACTION9chain 'L' and (resid 7 through 16 )
10X-RAY DIFFRACTION10chain 'L' and (resid 17 through 28 )

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