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- PDB-1jdp: Crystal Structure of Hormone/Receptor Complex -

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Basic information

Entry
Database: PDB / ID: 1jdp
TitleCrystal Structure of Hormone/Receptor Complex
Components
  • ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
  • C-TYPE NATRIURETIC PEPTIDE
KeywordsSIGNALING PROTEIN / hormone-receptor complex / natriuretic peptide receptor / allosteric activation
Function / homology
Function and homology information


cumulus cell differentiation / gastric emptying / c-di-GMP signaling / negative regulation of oocyte maturation / growth plate cartilage chondrocyte proliferation / growth plate cartilage chondrocyte differentiation / natriuretic peptide receptor activity / cellular response to glycoprotein / multicellular organismal locomotion / positive regulation of cGMP-mediated signaling ...cumulus cell differentiation / gastric emptying / c-di-GMP signaling / negative regulation of oocyte maturation / growth plate cartilage chondrocyte proliferation / growth plate cartilage chondrocyte differentiation / natriuretic peptide receptor activity / cellular response to glycoprotein / multicellular organismal locomotion / positive regulation of cGMP-mediated signaling / osteoclast proliferation / meiotic cell cycle process involved in oocyte maturation / receptor guanylyl cyclase signaling pathway / response to oxygen-glucose deprivation / cGMP biosynthetic process / negative regulation of meiotic cell cycle / negative regulation of collagen biosynthetic process / Physiological factors / hormone binding / regulation of osteoblast proliferation / regulation of smooth muscle cell proliferation / positive regulation of urine volume / negative regulation of DNA biosynthetic process / G protein-coupled peptide receptor activity / hormone receptor binding / cGMP-mediated signaling / negative regulation of cold-induced thermogenesis / chloride ion binding / peptide hormone binding / regulation of multicellular organism growth / blood vessel remodeling / response to axon injury / chromosome organization / positive regulation of osteoblast differentiation / post-embryonic development / ossification / blood vessel diameter maintenance / positive regulation of nitric-oxide synthase activity / secretory granule / skeletal system development / response to ischemia / peptide binding / hormone activity / regulation of blood pressure / intracellular calcium ion homeostasis / protein folding / angiogenesis / response to ethanol / negative regulation of neuron apoptotic process / response to hypoxia / response to xenobiotic stimulus / negative regulation of cell population proliferation / signaling receptor binding / signal transduction / protein homodimerization activity / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Natriuretic peptide, C 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 / Response regulator ...Natriuretic peptide, C 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 / 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 / C-type natriuretic peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Non-polymer description / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
B: ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR
H: C-TYPE NATRIURETIC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4459
Polymers101,2863
Non-polymers1,1596
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-29 kcal/mol
Surface area33090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.800, 136.455, 137.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Details(chain A + chain B + chain HA) or (Chain A + chain B + chain HB) For a single NPR-C monomer in the asymmetric unit, the chain identifier is A or B; For a CNP peptide the chain identifier is HA or HB ( each 0.5 occupancy ); for a biological assembly choose either A+B+HA or A+B+HB.

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABH

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


Mass: 49541.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRMHa3 / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / Strain (production host): S2 / References: UniProt: P17342
#2: Protein/peptide C-TYPE NATRIURETIC PEPTIDE / CNP


Mass: 2202.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / References: UniProt: P23582

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Sugars , 2 types, 4 molecules

#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.: 1
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 2 types, 472 molecules

#5: 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.: 470 / 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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
Conc.: 0.8 M / Common name: sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 70832 / Num. obs: 70832 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.6 / % possible all: 96.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 225890
Reflection shell
*PLUS
% possible obs: 96.6 %

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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: PDB ENTRY 1DP4

1dp4


Resolution: 2→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
Rfree0.248 3609 -random
Rwork0.227 ---
all-70832 --
obs-70832 97.7 %-
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-16 Å20 Å20 Å2
2---10.23 Å20 Å2
3----5.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6375 0 72 470 6917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.343 352 -
Rwork0.33 --
obs-6628 97.1 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.5 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.343 / Rfactor Rwork: 0.33

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