7BRH | pdb_00007brh

Atrial Natriuretic Peptide Receptor complexed with human Atrial Natriuretic Peptide

• PDB DOI: https://doi.org/10.2210/pdb7BRH/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus, Homo sapiens
• Expression System: Rattus norvegicus
• Mutation(s): No 


• Deposited: 2020-03-29 Released: 2021-03-31 
• Deposition Author(s): Ogawa, H.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural insight into hormone-recognition and transmembrane signaling by the atrial natriuretic peptide receptor

Ogawa, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 102.7 kDa 
• Atom Count: 7,470 
• Modeled Residue Count: 877 
• Deposited Residue Count: 898 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Atrial natriuretic peptide receptor 1	A, B	435	Rattus norvegicus	Mutation(s): 0  Gene Names: Npr1 EC: 4.6.1.2
UniProt
Find proteins for P18910 (Rattus norvegicus) Explore P18910  Go to UniProtKB:  P18910
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P18910-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Natriuretic peptides A	C [auth L]	28	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01160 (Homo sapiens) Explore P01160  Go to UniProtKB:  P01160
PHAROS:  P01160 GTEx:  ENSG00000175206

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], F [auth E]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth D], G [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL (Subject of Investigation/LOI)	H [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.209	α = 90
b = 100.209	β = 90
c = 261.721	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Ogawa, H.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP22570110
Japan Agency for Medical Research and Development (AMED)	Japan	JP17am0101080, JP18am0101080 and JP19am0101080

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary