5N86

Crystal structure of FAS1 domain of hyaluronic acid receptor stabilin-2

• PDB DOI: https://doi.org/10.2210/pdb5N86/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-23 Released: 2018-06-27 
• Deposition Author(s): Twarda-Clapa, A., Labuzek, B., Grudnik, P., Dubin, G., Holak, T.A.
• Funding Organization(s): National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Starting Model: experimental

Literature

Crystal structure of the FAS1 domain of the hyaluronic acid receptor stabilin-2.

Twarda-Clapa, A., Labuzek, B., Krzemien, D., Musielak, B., Grudnik, P., Dubin, G., Holak, T.A.

(2018) Acta Crystallogr D Struct Biol 74: 695-701

• PubMed: 29968679 
• DOI: https://doi.org/10.1107/S2059798318007271
• Primary Citation of Related Structures:  
  5N86


• PubMed Abstract: 
  

  Recent research has identified a potential role of the hyaluronic acid receptor stabilin-2 (Stab2) in cancer metastasis. Stab2 belongs to a group of scavenger receptors and is responsible for the clearance of more than ten ligands, including hyaluronic acid (HA). In vivo experiments on mice have shown that the absence of Stab2, or its blocking by an antibody, effectively opposes cancer metastasis, which is accompanied by an increase in the level of circulating HA. Knowledge of ligand recognition and signal transduction by Stab2 is limited and no three-dimensional structures of any protein fragments of this receptor have been solved to date. Here, a high-resolution X-ray structure of the seventh FAS1 domain of Stab2 is reported. This structure provides the first insight into the Stab2 structure.

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Organizational Affiliation: 

Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.45 kDa 
• Atom Count: 2,566 
• Modelled Residue Count: 279 
• Deposited Residue Count: 288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Stabilin-2	A, B	144	Homo sapiens	Mutation(s): 0  Gene Names: STAB2, FEEL2, FELL, FEX2, HARE
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWQ8 (Homo sapiens) Explore Q8WWQ8  Go to UniProtKB:  Q8WWQ8
PHAROS:  Q8WWQ8 GTEx:  ENSG00000136011

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 0.172 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.74	α = 90
b = 55.83	β = 90
c = 87.52	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data processing
SCALA	data scaling
PHENIX	refinement
MOLREP	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Twarda-Clapa, A., Labuzek, B., Grudnik, P., Dubin, G., Holak, T.A.

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Funding Organization	Location	Grant Number
National Science Centre	Poland	UMO-2015/17/N/NZ1/00025
National Science Centre	Poland	UMO-2012/06/A/ST5/00224

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description