6YAU | pdb_00006yau

CRYSTAL STRUCTURE OF ASGPR 1 IN COMPLEX WITH GN-A.

• PDB DOI: https://doi.org/10.2210/pdb6YAU/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-13 Released: 2021-01-13 
• Deposition Author(s): Schreuder, H.A., Liesum, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.219 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Triantennary GalNAc Molecular Imaging Probes for Monitoring Hepatocyte Function in a Rat Model of Nonalcoholic Steatohepatitis.

Mishra, A., Castaneda, T.R., Bader, E., Elshorst, B., Cummings, S., Scherer, P., Bangari, D.S., Loewe, C., Schreuder, H., Poverlein, C., Helms, M., Jones, S., Zech, G., Licher, T., Wagner, M., Schudok, M., de Hoop, M., Plowright, A.T., Atzrodt, J., Kannt, A., Laitinen, I., Derdau, V.

(2020) Adv Sci (Weinh) 7: 2002997-2002997

• PubMed: 33344141 
• DOI: https://doi.org/10.1002/advs.202002997
• Primary Citation of Related Structures:  
  6YAU, 6YG9


• PubMed Abstract: 
  

  Nonalcoholic steatohepatitis (NASH) is a progressive form of nonalcoholic fatty liver disease that can lead to irreversible liver cirrhosis and cancer. Early diagnosis of NASH is vital to detect disease before it becomes life-threatening, yet noninvasively differentiating NASH from simple steatosis is challenging. Herein, bifunctional probes have been developed that target the hepatocyte-specific asialoglycoprotein receptor (ASGPR), the expression of which decreases during NASH progression. The results show that the probes allow longitudinal, noninvasive monitoring of ASGPR levels by positron emission tomography in the newly developed rat model of NASH. The probes open new possibilities for research into early diagnosis of NASH and development of drugs to slow or reverse its progression.

---

Organizational Affiliation: 

Industriepark Höchst 65926 Frankfurt Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 18.54 kDa 
• Atom Count: 1,313 
• Modeled Residue Count: 129 
• Deposited Residue Count: 153 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asialoglycoprotein receptor 1	A	153	Homo sapiens	Mutation(s): 0  Gene Names: ASGR1, CLEC4H1
UniProt & NIH Common Fund Data Resources
Find proteins for P07306 (Homo sapiens) Explore P07306  Go to UniProtKB:  P07306
PHAROS:  P07306 GTEx:  ENSG00000141505

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OJB	E [auth A]	5-[(2~{R},3~{R},4~{R},5~{R},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-~{N}-[3-(propanoylamino)propyl]pentanamide C19 H35 N3 O8 IKUNNZGUTWUXRA-LQDZTQBFSA-N
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.219 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.75	α = 90
b = 32.53	β = 93.82
c = 39.65	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
BUSTER	refinement
autoPROC	data extraction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Schreuder, H.A., Liesum, A.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary