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- PDB-1jdn: Crystal Structure of Hormone Receptor -

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Basic information

Entry
Database: PDB / ID: 1jdn
TitleCrystal Structure of Hormone Receptor
ComponentsATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
KeywordsSIGNALING PROTEIN / Natriuretic peptide receptor / dimer / allosteric activation
Function / homology
Function and homology information


osteoclast proliferation / natriuretic peptide receptor activity / regulation of osteoblast proliferation / positive regulation of urine volume / G protein-coupled peptide receptor activity / negative regulation of cold-induced thermogenesis / chloride ion binding / hormone binding / peptide hormone binding / blood vessel remodeling ...osteoclast proliferation / natriuretic peptide receptor activity / regulation of osteoblast proliferation / positive regulation of urine volume / G protein-coupled peptide receptor activity / negative regulation of cold-induced thermogenesis / chloride ion binding / hormone binding / peptide hormone binding / blood vessel remodeling / positive regulation of nitric-oxide synthase activity / peptide binding / response to ischemia / skeletal system development / regulation of blood pressure / angiogenesis / signal transduction / protein homodimerization activity / protein-containing complex / extracellular exosome / plasma membrane
Similarity search - Function
: / Adenylyl cyclase class-4/guanylyl cyclase / Natriuretic peptides receptors signature. / Response regulator / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Atrial natriuretic peptide receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHe, X.-L. / Chow, D.-C. / Martick, M.M. / Garcia, K.C.
CitationJournal: Science / Year: 2001
Title: Allosteric activation of a spring-loaded natriuretic peptide receptor dimer by hormone.
Authors: He, X.l. / Chow, D.c. / Martick, M.M. / Garcia, K.C.
History
DepositionJun 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_chiral / 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_struct_assembly_gen.asym_id_list / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5815
Polymers49,5421
Non-polymers2,0394
Water00
1
A: ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
hetero molecules

A: ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,16110
Polymers99,0842
Non-polymers4,0778
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Unit cell
Length a, b, c (Å)217.189, 217.189, 130.793
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe second part of the biological assembly is generated by the two fold axis: -y, -x, -z+5/6.

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Components

#1: Protein ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR / NPR-C


Mass: 49541.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P17342
#2: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-4[DManpb1-6]DManpb1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-4-3-3/a4-b1_b4-c1_c4-d1_c6-f1_d4-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION


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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: potassium sodium phosphate, lithium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
Conc.: 1.5 M / Common name: sodium potassium phosphate / Details: or potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 43722 / Num. obs: 43722 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 86.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / % possible all: 98.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 217841
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.435

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The complex of this receptor with hormone being processed presently.

Resolution: 2.9→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2180 -Random
Rwork0.243 ---
all-43722 --
obs-43722 98.1 %-
Displacement parametersBiso mean: 65.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.15 Å213.77 Å20 Å2
2--12.15 Å20 Å2
3----24.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 134 0 3364
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.03
RfactorNum. reflection% reflection
Rfree0.389 170 -
Rwork0.367 --
obs-3291 98.4 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.243
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 65.8 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rfactor Rfree: 0.389 / Rfactor Rwork: 0.367

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