Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.58 kDa 
• Atom Count: 3364 
• Residue Count: 407 
• Unique protein chains: 1

1JDN

Crystal Structure of Hormone Receptor

• DOI: 10.2210/pdb1JDN/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2001-06-14 Released: 2001-09-05 
• Deposition Author(s): He, X.-L., Chow, D.-C., Martick, M.M., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.243 

Literature

Allosteric activation of a spring-loaded natriuretic peptide receptor dimer by hormone.

He, X.l., Chow, D.c., Martick, M.M., Garcia, K.C.

(2001) Science 293: 1657-1662

• PubMed: 11533490 
• DOI: 10.1126/science.1062246
• Primary Citation of Related Structures:  
  1JDP, 1JDN


• PubMed Abstract: 
  

Natriuretic peptides (NPs) are vasoactive cyclic-peptide hormones important in blood pressure regulation through interaction with natriuretic cell-surface receptors. We report the hormone-binding thermodynamics and crystal structures at 2.9 and 2.0 angstroms, respectively, of the extracellular domain of the unliganded human NP receptor (NPR-C) and its complex with CNP, a 22-amino acid NP. A single CNP molecule is bound in the interface of an NPR-C dimer, resulting in asymmetric interactions between the hormone and the symmetrically related receptors. Hormone binding induces a 20 angstrom closure between the membrane-proximal domains of the dimer. In each monomer, the opening of an interdomain cleft, which is tethered together by a linker peptide acting as a molecular spring, is likely a conserved allosteric trigger for intracellular signaling by the natriuretic receptor family.

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Organizational Affiliation: 

Departments of Microbiology and Immunology and Structural Biology, Stanford University School of Medicine, Fairchild D319, 299 Campus Drive, Stanford, CA 93405-5124, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATRIAL NATRIURETIC PEPTIDE CLEARANCE RECEPTOR	A	441	Homo sapiens	Mutation(s): 0  Gene Names: NPR3, ANPRC, C5orf23, NPRC
Find proteins for P17342 (Homo sapiens) Explore P17342  Go to UniProtKB:  P17342
NIH Common Fund Data Resources
PHAROS:  P17342 GTEx:  ENSG00000113389

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	B	6		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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	C	5		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.243 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 217.189	α = 90
b = 217.189	β = 90
c = 130.793	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-06-14 
• Released Date: 2001-09-05 
Deposition Author(s): He, X.-L., Chow, D.-C., Martick, M.M., Garcia, K.C.

Revision History 

• Version 1.0: 2001-09-05
  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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary