5IMK

Nanobody targeting human Vsig4 in Spacegroup C2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 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:  
    5IML, 5IMK, 5IMM, 5IMO

  • 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

    Department of Biochemistry and Molecular Biology, Key Laboratory of Environment and Genes Related to Diseases, Health Science Center, Xi'an Jiaotong University, Xi'an 710049, China. Electronic address: Fang.Zheng@xjtu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NanobodyB131CamelidaeMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
V-set and immunoglobulin domain-containing protein 4A220Homo sapiensMutation(s): 0 
Gene Names: VSIG4CRIgZ39IGUNQ317/PRO362
Find proteins for Q9Y279 (Homo sapiens)
Explore Q9Y279 
Go to UniProtKB:  Q9Y279
NIH Common Fund Data Resources
PHAROS  Q9Y279
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.791α = 90
b = 30.369β = 126.88
c = 84.297γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references