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- PDB-7brg: Atrial Natriuretic Peptide Receptor complexed with rat Atrial Nat... -

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Basic information

Entry
Database: PDB / ID: 7brg
TitleAtrial Natriuretic Peptide Receptor complexed with rat Atrial Natriuretic Peptide
Components
  • Atrial natriuretic peptide receptor 1
  • Natriuretic peptides A
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


Physiological factors / negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene ...Physiological factors / negative regulation of collecting lymphatic vessel constriction / : / ANPR-A receptor complex / natriuretic peptide receptor activity / : / neuropeptide receptor binding / : / mast cell granule / response to 3-methylcholanthrene / regulation of body fluid levels / receptor guanylyl cyclase signaling pathway / positive regulation of potassium ion export across plasma membrane / peptide receptor activity / guanylate cyclase / cell growth involved in cardiac muscle cell development / synaptic signaling via neuropeptide / cGMP biosynthetic process / guanylate cyclase activity / regulation of atrial cardiac muscle cell membrane repolarization / multicellular organismal-level water homeostasis / sodium ion export across plasma membrane / neuropeptide hormone activity / hormone receptor binding / negative regulation of systemic arterial blood pressure / glycinergic synapse / cardiac muscle hypertrophy in response to stress / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / : / dopamine metabolic process / hormone binding / peptide hormone binding / brush border / cellular response to angiotensin / neuropeptide signaling pathway / positive regulation of heart rate / negative regulation of blood pressure / positive regulation of cardiac muscle contraction / blood vessel diameter maintenance / cell projection / negative regulation of smooth muscle cell proliferation / cellular response to mechanical stimulus / female pregnancy / negative regulation of cell growth / response to insulin / hormone activity / regulation of blood pressure / vasodilation / cellular response to hydrogen peroxide / protein folding / heart development / perikaryon / response to hypoxia / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / signaling receptor binding / GTP binding / perinuclear region of cytoplasm / protein-containing complex / extracellular space / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : ...Natriuretic peptide, atrial type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / : / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Natriuretic peptides A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6809
Polymers99,9393
Non-polymers2,7416
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-14 kcal/mol
Surface area35740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.234, 100.234, 261.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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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 / Cell line (production host): HEK293T / Production host: Rattus norvegicus (Norway rat) / References: UniProt: P18910, guanylate cyclase
#2: Protein/peptide Natriuretic peptides A / Prepronatriodilatin


Mass: 3069.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P01161

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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, 150 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.8 Å3/Da / Density % sol: 67.63 %
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: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 52796 / % possible obs: 99.6 % / Redundancy: 22.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.5
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4463 / CC1/2: 0.56 / % possible all: 98.8

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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: 2.45→32.916 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2492 1519 2.88 %
Rwork0.1925 --
obs0.194 52690 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→32.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6887 0 180 148 7215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067516
X-RAY DIFFRACTIONf_angle_d0.78510232
X-RAY DIFFRACTIONf_dihedral_angle_d13.6614448
X-RAY DIFFRACTIONf_chiral_restr0.0451134
X-RAY DIFFRACTIONf_plane_restr0.0041320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.52910.31371600.30624690X-RAY DIFFRACTION99
2.5291-2.61940.38491580.2984771X-RAY DIFFRACTION99
2.6194-2.72430.35241530.29374762X-RAY DIFFRACTION99
2.7243-2.84820.36991520.26334755X-RAY DIFFRACTION100
2.8482-2.99820.32661170.24864796X-RAY DIFFRACTION100
2.9982-3.18590.30821140.24234812X-RAY DIFFRACTION99
3.1859-3.43170.24991420.22494701X-RAY DIFFRACTION98
3.4317-3.77660.30061570.19774591X-RAY DIFFRACTION96
3.7766-4.3220.21251320.16264543X-RAY DIFFRACTION94
4.322-5.44130.18891220.14524463X-RAY DIFFRACTION93
5.4413-32.9160.20681120.16584287X-RAY DIFFRACTION88
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)
10.0566-0.0022-0.02690.21090.1140.171-0.17780.0938-0.05880.0042-0.2581-0.349-0.27820.1799-0.4170.7641-0.10740.02410.42740.32160.726739.964512.8083-8.2281
20.07890.1286-0.02680.14910.00340.0664-0.13840.22690.1731-0.04020.19310.2833-0.0383-0.009300.65450.0340.04150.43690.17660.482911.33768.9891-15.4623
30.13010.1015-0.08970.2708-0.03520.1708-0.03460.13370.3375-0.09570.07490.1698-0.71870.0276-0.02270.9943-0.1038-0.04880.37030.370.662825.582122.644-16.1692
40.15310.012-0.08420.2243-0.07610.096-0.1365-0.15360.06360.0869-0.1887-0.56350.02080.3618-0.15570.73950.2087-0.05350.34890.50890.796743.7479-11.49139.612
50.1318-0.2120.10810.2555-0.11510.1531-0.1394-0.2591-0.2652-0.04990.08450.15430.21570.0433-0.00250.7202-0.0352-0.02260.41160.15720.557813.8102-10.594213.5125
60.096-0.13020.10440.3835-0.05270.1552-0.055-0.117-0.28640.10970.03010.11360.7393-0.0242-0.09791.03490.09590.05880.36660.35370.625725.5789-22.63916.3543
70.00030.0005-0.00060.0052-0.00620.00540.0379-0.0012-0.00640.00130.02180.01260.00370.0143-01.17390.01370.00820.70160.08790.729616.3666-0.00810.0999
8-0.00060.0002-0.00050.0068-0.00450.00270.0048-0.0088-0.00120.0019-0.0186-0.00190.0043-0.0196-01.0350.00970.02150.63180.1670.526823.7982-0.00720.0918
90.00140.0005-0.0001-0.0001-0.00140.00170.0279-0.0034-0.0076-0.00510.0508-0.02470.0052-0.004100.5185-0.0067-0.00290.57690.13010.323813.54030.00470.0974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 142 )
2X-RAY DIFFRACTION2chain 'A' and (resid 143 through 266 )
3X-RAY DIFFRACTION3chain 'A' and (resid 267 through 426 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 266 )
6X-RAY DIFFRACTION6chain 'B' and (resid 267 through 426 )
7X-RAY DIFFRACTION7chain 'L' and (resid 4 through 8 )
8X-RAY DIFFRACTION8chain 'L' and (resid 9 through 23 )
9X-RAY DIFFRACTION9chain 'L' and (resid 24 through 28 )

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