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- PDB-1dp4: DIMERIZED HORMONE BINDING DOMAIN OF THE ATRIAL NATRIURETIC PEPTID... -

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Basic information

Entry
Database: PDB / ID: 1dp4
TitleDIMERIZED HORMONE BINDING DOMAIN OF THE ATRIAL NATRIURETIC PEPTIDE RECEPTOR
ComponentsATRIAL NATRIURETIC PEPTIDE RECEPTOR A
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / LYASE / periplasmic binding protein fold / dimer / LYASE COMPLEX / HORMONE-GROWTH FACTOR RECEPTOR
Function / homology
Function and homology information


Physiological factors / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / hormone binding ...Physiological factors / ANPR-A receptor complex / natriuretic peptide receptor activity / positive regulation of cGMP-mediated signaling / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / cGMP biosynthetic process / guanylate cyclase activity / 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 / regulation of blood pressure / cell surface receptor signaling pathway / receptor complex / protein kinase activity / intracellular signal transduction / GTP binding / ATP binding / plasma membrane
Similarity search - Function
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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Response regulator ...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 / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Response regulator / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
Authorsvan den Akker, F. / Zhang, X. / Miyagi, M. / Huo, X. / Misono, K.S. / Yee, V.C.
CitationJournal: Nature / Year: 2000
Title: Structure of the dimerized hormone-binding domain of a guanylyl-cyclase-coupled receptor.
Authors: van den Akker, F. / Zhang, X. / Miyagi, M. / Huo, X. / Misono, K.S. / Yee, V.C.
History
DepositionDec 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
C: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,72418
Polymers96,8702
Non-polymers2,85416
Water9,260514
1
C: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
hetero molecules

C: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,04120
Polymers96,8702
Non-polymers3,17218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area5480 Å2
ΔGint-91 kcal/mol
Surface area37930 Å2
MethodPISA
2
A: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
hetero molecules

A: ATRIAL NATRIURETIC PEPTIDE RECEPTOR A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,40716
Polymers96,8702
Non-polymers2,53714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5410 Å2
ΔGint-114 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.250, 120.250, 160.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-649-

HOH

DetailsTHE DIMER IN THIS ENTRY IS THE HEAD TO HEAD (HH)-DIMER THAT HAS SUBSEQUENTLY BEEN IDENTIFIED AS THE PHYSIOLOGICALLY ACTIVE DIMER BY SITE-DIRECTED MUTAGENESIS STUDIES (QIU, Y., OGAWA, H., ZHANG, X., MISONO, K.S. J.BIOL.CHEM. 279:6115-23, 2004) AND THE DIMER IN SOLUTION BY ELECTRON MICROSCOPY COUPLED WITH SINGLE PARTICLE RECONSTRUCTION (SUBMITTED FOR PUBLICATION). THE CC DIMER (biolomecule 1) WAS CHOSEN by author FOR A SLIGHTLY LARGER BURIED SURFACE AREA AND MORE CARBOXYL TERMINAL STRUCTURE ASSIGNED.

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein ATRIAL NATRIURETIC PEPTIDE RECEPTOR A


Mass: 48434.828 Da / Num. of mol.: 2 / Fragment: HORMONE BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PCDNA3-NPR / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P18910, guanylate cyclase

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Sugars , 2 types, 5 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 525 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.4
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMHEPES1drop
30.1 MTris-HCl1reservoir
40.2 M1reservoirLi2SO4
526 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 80413 / Num. obs: 79776 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 32
Reflection shellResolution: 2→2.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.285 / Num. unique all: 12036 / % possible all: 96.8
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNS0.5refinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3501141.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3965 5.1 %RANDOM
Rwork0.198 ---
all-80496 --
obs-78461 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.45 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6720 0 173 514 7407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 648 5.1 %
Rwork0.213 12036 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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