5IMK

Nanobody targeting human Vsig4 in Spacegroup C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.227 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural evaluation of a nanobody targeting complement receptor Vsig4 and its cross reactivity

Wen, Y.Ouyang, Z.Schoonooghe, S.Luo, S.De Baetselier, P.Lu, W.Muyldermans, S.Raes, G.Zheng, F.

(2017) Immunobiology 222: 807-813

  • DOI: 10.1016/j.imbio.2016.11.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Vsig4 is a recently identified immune regulatory protein related to the B7 family with dual functionality: a negative regulator of T cell activation and a receptor for the complement components C3b and C3c. Here we present a structural evaluation of ...

    Vsig4 is a recently identified immune regulatory protein related to the B7 family with dual functionality: a negative regulator of T cell activation and a receptor for the complement components C3b and C3c. Here we present a structural evaluation of a nanobody, Nb119, against the extracellular IgV domain protein of both mouse and human recombinant Vsig4, which have a high degree of sequence identity. Although mouse and human Vsig4 bind to Nb119 with a 250 times difference in dissociation constants, the interaction results in a highly identical assembly with a RMSD of 0.4Å. The molecular determinants for Vsig4 recognition and cross reactivity unveiled by the atomic structure of Nb119 in complex with mVsig4 and hVsig4 afford new insights useful for the further optimization of the nanobody for potential use in humans. Additionally, structural analysis of the Vsig4-Nb119 complexes indicates that Nb119 occupies the interface on Vsig4 recognized by the macroglobulin-like domains MG4 and MG5 of C3b. Thus an affinity-improved Nb119 may have the potential to influence the activation of both T cells and complement.


    Organizational Affiliation

    Center for Translational Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nanobody
B
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
V-set and immunoglobulin domain-containing protein 4
A
220Homo sapiensMutation(s): 0 
Gene Names: VSIG4 (CRIg, Z39IG)
Find proteins for Q9Y279 (Homo sapiens)
Go to Gene View: VSIG4
Go to UniProtKB:  Q9Y279
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.227 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.791α = 90.00
b = 30.369β = 126.88
c = 84.297γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-03-06 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Wen, Y.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-07-05
    Type: Database references