Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 12.08 kDa 
• Atom Count: 802 
• Modelled Residue Count: 104 
• Deposited Residue Count: 113 
• Unique protein chains: 1

5JFB

Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163

• PDB DOI: 10.2210/pdb5JFB/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Sus scrofa
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2016-04-19 Released: 2017-03-22 
• Deposition Author(s): Ma, H., Jiang, L., Qiao, S., Zhang, G., Li, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

The Crystal Structure of the Fifth Scavenger Receptor Cysteine-Rich Domain of Porcine CD163 Reveals an Important Residue Involved in Porcine Reproductive and Respiratory Syndrome Virus Infection

Ma, H., Jiang, L., Qiao, S., Zhi, Y., Chen, X.X., Yang, Y., Huang, X., Huang, M., Li, R., Zhang, G.P.

(2017) J Virol 91

• PubMed: 27881657 
• DOI: 10.1128/JVI.01897-16
• Primary Citation of Related Structures:  
  5JFB


• PubMed Abstract: 
  

Porcine reproductive and respiratory syndrome (PRRS) has become an economically critical factor in swine industry since its worldwide spread in the 1990s. Infection by its causative agent, PRRS virus (PRRSV), was proven to be mediated by an indispensable receptor, porcine CD163 (pCD163), and the fifth scavenger receptor cysteine-rich domain (SRCR5) is essential for virus infection. However, the structural details and specific residues of pCD163 SRCR5 involved in infection have not been defined yet. In this study, we prepared recombinant pCD163 SRCR5 in Drosophila melanogaster Schneider 2 (S2) cells and determined its crystal structure at a high resolution of 2.0 Å. This structure includes a markedly long loop region and shows a special electrostatic potential, and these are significantly different from those of other members of the scavenger receptor cysteine-rich superfamily (SRCR-SF). Subsequently, we carried out structure-based mutational studies to identify that the arginine residue at position 561 (Arg561) in the long loop region is important for PRRSV infection. Further, we showed Arg561 probably takes effect on the binding of pCD163 to PRRSV during virus invasion. Altogether the current work provides the first view of the CD163 SRCR domain, expands our knowledge of the invasion mechanism of PRRSV, and supports a molecular basis for prevention and control of the virus.

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Organizational Affiliation: 

Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Scavenger receptor cysteine-rich type 1 protein M130	A	113	Sus scrofa	Mutation(s): 0  Gene Names: CD163, M130
UniProt
Find proteins for Q2VL90 (Sus scrofa) Explore Q2VL90  Go to UniProtKB:  Q2VL90

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.711	α = 90
b = 73.93	β = 90
c = 87.527	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data processing
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-04-19 
• Released Date: 2017-03-22 
Deposition Author(s): Ma, H., Jiang, L., Qiao, S., Zhang, G., Li, R.

Revision History  

• Version 1.0: 2017-03-22
  Type: Initial release