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- PDB-7brl: Atrial Natriuretic Peptide Receptor complexed with Deletion mutan... -

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Basic information

Entry
Database: PDB / ID: 7brl
TitleAtrial Natriuretic Peptide Receptor complexed with Deletion mutant of rat Atrial Natriuretic Peptide[4-17,23]
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: 3.2 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 30, 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)101,2129
Polymers98,4713
Non-polymers2,7416
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-8 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.273, 100.273, 270.415
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#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 / Atrial natriuretic factor prohormone / proANF / Atrial natriuretic peptide prohormone / proANP / ...Atrial natriuretic factor prohormone / proANF / Atrial natriuretic peptide prohormone / proANP / Atriopeptigen / Cardiodilatin / CDD / preproCDD-ANF


Mass: 1600.848 Da / Num. of mol.: 1 / Mutation: deletions of residues 1-3, 18-22 and 24-28 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P01161
#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
#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
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: 3.99 Å3/Da / Density % sol: 69.14 %
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: 3.2→50 Å / Num. obs: 24713 / % possible obs: 97.4 % / Redundancy: 23.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 27.6
Reflection shellResolution: 3.2→3.29 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2096 / CC1/2: 0.42

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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: 3.2→33.517 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 32.8
RfactorNum. reflection% reflection
Rfree0.2367 761 3.08 %
Rwork0.1982 --
obs0.1995 24700 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→33.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6808 0 180 0 6988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077354
X-RAY DIFFRACTIONf_angle_d0.82210016
X-RAY DIFFRACTIONf_dihedral_angle_d12.2294358
X-RAY DIFFRACTIONf_chiral_restr0.0461116
X-RAY DIFFRACTIONf_plane_restr0.0051290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.44690.39571450.30724879X-RAY DIFFRACTION99
3.4469-3.79330.30641440.24914857X-RAY DIFFRACTION99
3.7933-4.34120.23651710.19454848X-RAY DIFFRACTION99
4.3412-5.46560.22341530.18054585X-RAY DIFFRACTION94
5.4656-33.5170.19861480.17224770X-RAY DIFFRACTION96
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)
10.0843-0.03860.05990.1456-0.02890.1024-0.06230.06140.0070.08860.01660.0296-0.19220.53940.02731.1338-0.43380.07950.30460.15780.498147.071511.6053-12.9711
20.0218-0.0056-0.01710.1580.14530.16570.1425-0.2019-0.08180.44880.00580.5293-0.5968-0.1-0.13581.42630.03210.15680.21410.16180.686328.424812.618-5.4941
30.270.1869-0.07850.17080.02710.1208-0.1820.06980.65740.12230.17520.4154-0.6327-0.22970.00870.96380.23910.09590.53160.18541.07312.31339.6811-19.0783
40.12280.095-0.01270.39150.32880.4975-0.02090.29990.52170.0084-0.02170.6332-1.4797-0.0014-0.12761.6995-0.0793-0.00440.25990.3230.887328.248922.9997-15.9397
50.1634-0.0371-0.22410.2080.05040.34960.00410.0235-0.0033-0.44320.22250.1160.37990.44530.32141.32520.4375-0.1121-0.0280.41930.220544.5055-11.22259.925
60.5391-0.30020.00870.18350.09990.2861-0.0506-0.1973-0.4729-0.29060.14680.61030.8978-0.37480.06351.0406-0.2517-0.16080.43990.16761.116914.5963-10.97215.996
70.1263-0.047-0.04350.31940.32870.4757-0.0752-0.341-0.5656-0.0934-0.0030.48191.3790.1061-0.16111.65740.0374-0.03630.26520.31760.861828.2773-23.015816.1373
80.0101-0.0017-0.00990.0030.00390.01250.0081-0.005-0.0071-0.006-0.0584-0.00410.00710.1162-0.01280.91490.01540.06770.38910.1651-0.008923.0805-0.04190.0863
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 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 287 )
4X-RAY DIFFRACTION4chain 'A' and (resid 288 through 426 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 115 )
6X-RAY DIFFRACTION6chain 'B' and (resid 116 through 287 )
7X-RAY DIFFRACTION7chain 'B' and (resid 288 through 426 )
8X-RAY DIFFRACTION8chain 'L' and (resid 4 through 23 )

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