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- PDB-7bri: Atrial Natriuretic Peptide Receptor complexed with Dendroaspis Na... -

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Basic information

Entry
Database: PDB / ID: 7bri
TitleAtrial Natriuretic Peptide Receptor complexed with Dendroaspis Natriuretic Peptide
Components
  • Atrial natriuretic peptide receptor 1
  • Natriuretic peptide DNP
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 / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / hormone binding ...ANPR-A receptor complex / Physiological factors / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / hormone binding / adenylate cyclase activity / dopamine metabolic process / cGMP-mediated signaling / peptide hormone binding / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / hormone activity / regulation of blood pressure / vasodilation / toxin activity / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / GTP binding / extracellular region / ATP binding / plasma membrane
Similarity search - Function
Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / 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 ...Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / 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
Atrial natriuretic peptide receptor 1 / Natriuretic peptide DNP
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Dendroaspis angusticeps (eastern green mamba)
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

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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 peptide DNP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8119
Polymers101,0693
Non-polymers2,7416
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-24 kcal/mol
Surface area35650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.597, 99.597, 262.467
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 peptide DNP


Mass: 4199.708 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P28374

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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, 142 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.: 140 / 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: 3.72 Å3/Da / Density % sol: 66.92 %
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: Dec 19, 2010
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: 51990 / % possible obs: 96.3 % / Redundancy: 22.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.053 / Net I/σ(I): 30
Reflection shellResolution: 2.45→2.52 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 4457 / CC1/2: 0.66

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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→30.711 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2.1 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2408 1496 2.88 %
Rwork0.2007 --
obs0.2018 51983 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→30.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6917 0 180 140 7237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067690
X-RAY DIFFRACTIONf_angle_d0.82910486
X-RAY DIFFRACTIONf_dihedral_angle_d13.1884562
X-RAY DIFFRACTIONf_chiral_restr0.0471168
X-RAY DIFFRACTIONf_plane_restr0.0061356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5290.31221620.29034718X-RAY DIFFRACTION100
2.529-2.61940.29481580.28014737X-RAY DIFFRACTION100
2.6194-2.72420.32671420.27524705X-RAY DIFFRACTION100
2.7242-2.84810.33121490.25614747X-RAY DIFFRACTION100
2.8481-2.99810.28691180.24244758X-RAY DIFFRACTION100
2.9981-3.18580.27331170.22564728X-RAY DIFFRACTION99
3.1858-3.43150.24491380.20834653X-RAY DIFFRACTION98
3.4315-3.77630.25111530.18964420X-RAY DIFFRACTION94
3.7763-4.32140.22311340.16664380X-RAY DIFFRACTION92
4.3214-5.43960.17461120.15124299X-RAY DIFFRACTION90
5.4396-30.7110.18521130.17314342X-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)
10.99311.1135-0.7512.7826-0.48781.43390.029-0.0268-0.12690.0019-0.2327-0.7627-0.2130.5230.19280.5466-0.09930.04590.34090.2940.657243.262911.4854-9.1798
22.26481.36660.65233.37430.32311.802-0.12560.35670.7587-0.2213-0.03550.7747-0.3132-0.21680.0230.51970.055-0.0020.2830.1560.60613.435311.1759-14.5759
31.04640.4973-0.33662.66160.22021.07760.04590.18330.3805-0.1413-0.03890.4769-0.5674-0.0894-0.16310.8023-0.07060.00780.29650.27440.719327.077723.528-14.7706
40.9938-0.95310.74932.6061-0.46921.36850.01440.00310.0680.0115-0.233-0.72090.240.5330.18510.57570.1041-0.05080.34410.29670.65443.263-11.43769.8968
52.1676-1.3922-0.58683.42240.41531.7703-0.1443-0.36-0.79320.1779-0.0280.81020.3411-0.24940.0410.5154-0.0458-0.00890.28710.16330.606813.4181-11.112715.253
60.962-0.30450.2862.62430.1341.10510.0317-0.1524-0.31260.1236-0.01590.5160.6061-0.0784-0.20.80750.0856-0.01290.30240.27670.716227.0601-23.476415.4536
70-0.00050.00070.0018-0.00190.00280.03690.0003-0.00160.00130.01750.00550.0001-0.00500.51110.0062-0.01560.38850.07260.256718.39810.02880.3464
80.00010.00070.00020.01670.00650.00250.0040.0003-0.0022-0.0019-0.0131-0.00910.00170.0033-0.03060.3616-0.01050.00590.12790.08840.263920.89990.02170.3658
9-0.00010.0001-0.00010.0008-0.0010.00110.01290.00280.00310.00290.013-0.0117-0.00190.0072-00.3557-0.0019-0.00140.32050.08310.18514.90790.01340.4073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 287 )
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 426 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 115 )
5X-RAY DIFFRACTION5chain 'B' and (resid 116 through 287 )
6X-RAY DIFFRACTION6chain 'B' and (resid 288 through 426 )
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 5 )
8X-RAY DIFFRACTION8chain 'L' and (resid 6 through 25 )
9X-RAY DIFFRACTION9chain 'L' and (resid 26 through 29 )

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