1DP4 | pdb_00001dp4

DIMERIZED HORMONE BINDING DOMAIN OF THE ATRIAL NATRIURETIC PEPTIDE RECEPTOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.208 (DCC) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structure of the dimerized hormone-binding domain of a guanylyl-cyclase-coupled receptor.

van den Akker, F.Zhang, X.Miyagi, M.Huo, X.Misono, K.S.Yee, V.C.

(2000) Nature 406: 101-104

  • DOI: https://doi.org/10.1038/35017602
  • Primary Citation Related Structures: 
    1DP4

  • PubMed Abstract: 

    The atrial natriuretic peptide (ANP) hormone is secreted by the heart in response to an increase in blood pressure. ANP exhibits several potent anti-hypertensive actions in the kidney, adrenal gland and vascular system. These actions are induced by hormone binding extracellularly to the ANP receptor, thereby activating its intracellular guanylyl cyclase domain for the production of cyclic GMP. Here we present the crystal structure of the glycosylated dimerized hormone-binding domain of the ANP receptor at 2.0-A resolution. The monomer comprises two interconnected subdomains, each encompassing a central beta-sheet flanked by alpha-helices, and exhibits the type I periplasmic binding protein fold. Dimerization is mediated by the juxtaposition of four parallel helices, arranged two by two, which brings the two protruding carboxy termini into close relative proximity. From affinity labelling and mutagenesis studies, the ANP-binding site maps to the side of the dimer crevice and extends to near the dimer interface. A conserved chloride-binding site is located in the membrane distal domain, and we found that hormone binding is chloride dependent. These studies suggest mechanisms for hormone activation and the allostery of the ANP receptor.


  • Organizational Affiliation
    • Department of Molecular Biology, Lerner Research Institute, Cleveland Clinic Foundation, Ohio 44195, USA.

Macromolecule Content 

  • Total Structure Weight: 99.72 kDa 
  • Atom Count: 7,445 
  • Modeled Residue Count: 854 
  • Deposited Residue Count: 870 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATRIAL NATRIURETIC PEPTIDE RECEPTOR AA,
B [auth C]
435Rattus norvegicusMutation(s): 0 
EC: 4.6.1.2
UniProt
Find proteins for P18910 (Rattus norvegicus)
Explore P18910 
Go to UniProtKB:  P18910
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18910
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P18910-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B],
D,
E,
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
L [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth C]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
R [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.225 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.208 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.25α = 90
b = 120.25β = 90
c = 160.55γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary