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- PDB-7brh: Atrial Natriuretic Peptide Receptor complexed with human Atrial N... -

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Basic information

Entry
Database: PDB / ID: 7brh
TitleAtrial Natriuretic Peptide Receptor complexed with human 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 / 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 / negative regulation of JUN kinase activity / regulation of atrial cardiac muscle cell membrane repolarization / Physiological factors / cardiac conduction system development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / 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 / aortic valve morphogenesis / 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 / response to muscle stretch / positive regulation of cardiac muscle contraction / blood vessel diameter maintenance / cell projection / negative regulation of smooth muscle cell proliferation / female pregnancy / cellular response to mechanical stimulus / negative regulation of cell growth / response to insulin / hormone activity / regulation of blood pressure / vasodilation / cellular response to hydrogen peroxide / protein folding / : / perikaryon / response to hypoxia / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / Amyloid fiber formation / signaling receptor binding / GTP binding / perinuclear region of cytoplasm / protein-containing complex / extracellular space / extracellular region / 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)
Homo sapiens (human)
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)102,6999
Polymers99,9573
Non-polymers2,7416
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-15 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.209, 100.209, 261.721
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 Natriuretic peptides A / CDD-ANF / Cardiodilatin / CDD / Cardiodilatin-related peptide / CDP / Prepronatriodilatin


Mass: 3087.505 Da / Num. of mol.: 1 / 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, 148 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.: 146 / 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: 67.59 %
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: May 24, 2009
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: 52731 / % possible obs: 96.8 % / Redundancy: 27.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.9
Reflection shellResolution: 2.45→2.52 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4442 / CC1/2: 0.51

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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→43.449 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2375 1526 2.89 %
Rwork0.195 --
obs0.1962 52725 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→43.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6887 0 180 146 7213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067516
X-RAY DIFFRACTIONf_angle_d0.78310230
X-RAY DIFFRACTIONf_dihedral_angle_d13.164450
X-RAY DIFFRACTIONf_chiral_restr0.0471132
X-RAY DIFFRACTIONf_plane_restr0.0051320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.52910.321630.30354668X-RAY DIFFRACTION98
2.5291-2.61950.35311560.29654735X-RAY DIFFRACTION99
2.6195-2.72440.29071480.28684727X-RAY DIFFRACTION99
2.7244-2.84830.34891510.25844771X-RAY DIFFRACTION100
2.8483-2.99850.33311170.25624804X-RAY DIFFRACTION100
2.9985-3.18630.30191140.24824825X-RAY DIFFRACTION100
3.1863-3.43220.25561470.23764697X-RAY DIFFRACTION98
3.4322-3.77740.31321550.20974595X-RAY DIFFRACTION96
3.7774-4.32360.2051420.17084542X-RAY DIFFRACTION94
4.3236-5.44560.16731230.14814459X-RAY DIFFRACTION93
5.4456-43.44490.18551100.15724376X-RAY DIFFRACTION90
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)
10.0533-0.0367-0.00810.02560.00340.0099-0.11680.0429-0.0702-0.0582-0.09-0.25020.00090.2539-0.10860.7222-0.13080.18320.45540.49850.864346.128512.0005-12.7103
20.01970.0017-0.04380.0610.0590.19490.0426-0.01960.08010.2761-0.1569-0.2272-0.3640.1648-0.23230.7765-0.0171-0.00470.17690.27340.503326.067212.7182-4.4502
30.01870.0415-0.00460.0538-0.00010.0096-0.22990.12830.265-0.22930.15630.3295-0.0634-0.1028-0.00230.7211-0.0041-0.00150.47610.18210.44819.61788.1441-19.1784
40.11080.1595-0.10080.3814-0.09050.1107-0.0330.1610.3498-0.07780.03120.0293-0.65910.0237-0.13151.0111-0.0652-0.0040.31920.37910.613225.551122.6541-16.1312
50.13510.0178-0.07020.2174-0.10480.1732-0.1461-0.06680.03370.0104-0.1936-0.54690.21220.3962-0.4680.73430.1672-0.01260.34110.49110.784939.9111-12.80668.4037
60.102-0.12220.01250.12130.01570.0445-0.1193-0.2054-0.18690.08670.19610.32030.1121-0.05210.00530.6457-0.0311-0.01030.37250.21010.454811.3171-9.020515.6314
70.1161-0.11580.06980.2953-0.03490.088-0.0429-0.2002-0.31880.08980.01290.05610.6486-0.0287-0.04511.03360.09810.03250.3460.41320.611825.5471-22.651816.343
80.0005-0.00050.00020.011-0.01150.00720.03090.00170.0005-0.00180.0051-0.0196-0.00680.0048-01.0367-0.00340.00770.40860.15780.399723.127-0.01880.0999
90.0055-0.0006-0.0051-0.0015-0.00030.00410.02680.007-0.0007-0.01120.01360.00460.0171-0.0170.03480.58810.02280.01190.46360.21960.273815.8597-0.00030.0993
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 142 )
6X-RAY DIFFRACTION6chain 'B' and (resid 143 through 266 )
7X-RAY DIFFRACTION7chain 'B' and (resid 267 through 426 )
8X-RAY DIFFRACTION8chain 'L' and (resid 4 through 16 )
9X-RAY DIFFRACTION9chain 'L' and (resid 17 through 28 )

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