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- PDB-1t34: ROTATION MECHANISM FOR TRANSMEMBRANE SIGNALING BY THE ATRIAL NATR... -

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Basic information

Entry
Database: PDB / ID: 1t34
TitleROTATION MECHANISM FOR TRANSMEMBRANE SIGNALING BY THE ATRIAL NATRIURETIC PEPTIDE RECEPTOR
Components
  • Atrial natriuretic peptide factor
  • Atrial natriuretic peptide receptor A
KeywordsSIGNALING PROTEIN / MEMBRANE PROTEIN / RECEPTOR-HORMONE COMPLEX / NATRIURETIC PEPTIDE RECEPTOR / GUANYLYL-CYCLASE-COUPLED RECEPTOR / SIGNAL TRANSDUCTION / ROTATION MECHANISM
Function / homology
Function and homology information


negative regulation of collecting lymphatic vessel constriction / ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of histamine secretion by mast cell / positive regulation of cGMP-mediated signaling / mast cell granule / synaptic signaling via neuropeptide / receptor guanylyl cyclase signaling pathway ...negative regulation of collecting lymphatic vessel constriction / ANPR-A receptor complex / Physiological factors / positive regulation of delayed rectifier potassium channel activity / natriuretic peptide receptor activity / positive regulation of histamine secretion by mast cell / positive regulation of cGMP-mediated signaling / mast cell granule / synaptic signaling via neuropeptide / receptor guanylyl cyclase signaling pathway / peptide receptor activity / response to 3-methylcholanthrene / regulation of body fluid levels / neuropeptide receptor binding / guanylate cyclase / regulation of high voltage-gated calcium channel activity / positive regulation of potassium ion export across plasma membrane / guanylate cyclase activity / cGMP biosynthetic process / cell growth involved in cardiac muscle cell development / regulation of atrial cardiac muscle cell membrane repolarization / hormone binding / sodium ion export across plasma membrane / multicellular organismal-level water homeostasis / glycinergic synapse / neuropeptide hormone activity / negative regulation of systemic arterial blood pressure / cardiac muscle hypertrophy in response to stress / adenylate cyclase activity / hormone receptor binding / cellular response to angiotensin / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / positive regulation of heart rate / dopamine metabolic process / cGMP-mediated signaling / brush border / peptide hormone binding / neuropeptide signaling pathway / positive regulation of cardiac muscle contraction / negative regulation of blood pressure / blood vessel diameter maintenance / cell projection / female pregnancy / negative regulation of smooth muscle cell proliferation / response to insulin / hormone activity / negative regulation of cell growth / cellular response to hydrogen peroxide / regulation of blood pressure / vasodilation / cellular response to mechanical stimulus / 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 / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. ...Natriuretic peptide, atrial type / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / 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 / 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
Natriuretic peptides A / Atrial natriuretic peptide receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsOgawa, H. / Qiu, Y. / Ogata, C.M. / Misono, K.S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of hormone-bound atrial natriuretic peptide receptor extracellular domain: rotation mechanism for transmembrane signal transduction
Authors: Ogawa, H. / Qiu, Y. / Ogata, C.M. / Misono, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and preliminary x-ray analysis of atrial natriuretic peptide (anp) receptor extracellular domain complex with anp: use of ammonium sulfate as the cryosalt
Authors: Ogawa, H. / Zhang, X. / Qiu, Y. / Ogata, C.M. / Misono, K.S.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Constitutive activation and uncoupling of the atrial natriuretic peptide receptor by mutations at the dimer interface: role of dimer interface in signaling
Authors: Qiu, Y. / Ogawa, H. / Miyagi, M. / Misono, K.S.
History
DepositionApr 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Atrial natriuretic peptide receptor A
B: Atrial natriuretic peptide receptor A
H: Atrial natriuretic peptide factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8569
Polymers99,0873
Non-polymers1,7696
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-25 kcal/mol
Surface area36400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.131, 100.131, 259.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein Atrial natriuretic peptide receptor A / ANP-A / ANPRA / GC-A / Guanylate cyclase / NPR-A / Atrial natriuretic peptide A-type receptor


Mass: 48434.828 Da / Num. of mol.: 2 / Fragment: HORMONE BINDING DOMAIN (RESIDUES 1-435)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NPR1 / Plasmid: PCDNA3-NPRA-ECD / Cell (production host): Baby Hampster Kidney Cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P18910
#2: Protein/peptide Atrial natriuretic peptide factor / ANF / ANP / Prepronatriodilatin / Atrial natriuretic peptide


Mass: 2217.515 Da / Num. of mol.: 1 / Fragment: RESIDUES 129-149 / Source method: obtained synthetically / Details: This sequence occurs in Rattus norvegicus / References: UniProt: P01161
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.21 Å3/Da / Density % sol: 67 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: AMMONIUM SULFATE, SODIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979338 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.95→87.71 Å / Num. all: 30886 / Num. obs: 25503 / % possible obs: 93.7 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.9
Reflection shellResolution: 2.95→3.04 Å / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.2 / % possible all: 89.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DP4

1dp4


Resolution: 2.95→87.71 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.902 / SU B: 20.514 / SU ML: 0.378 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26857 2123 7.7 %RANDOM
Rwork0.23745 ---
all0.2399 30886 --
obs0.23745 25503 89.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.512 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.95→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 114 0 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217280
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9699910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1615884
X-RAY DIFFRACTIONr_chiral_restr0.0840.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025586
X-RAY DIFFRACTIONr_nbd_refined0.2430.23436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2220
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.235
X-RAY DIFFRACTIONr_mcbond_it1.5591.54418
X-RAY DIFFRACTIONr_mcangle_it2.9437090
X-RAY DIFFRACTIONr_scbond_it2.47832862
X-RAY DIFFRACTIONr_scangle_it3.54932820
LS refinement shellResolution: 2.95→3.05 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.301 168
Rwork0.269 2039

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