5N48

Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Anticalins Reveal High Plasticity in the Mode of Complex Formation with a Common Tumor Antigen.

Schiefner, A.Gebauer, M.Richter, A.Skerra, A.

(2018) Structure 26: 649-656.e3

  • DOI: 10.1016/j.str.2018.02.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the comparative X-ray structural analysis of three Anticalin proteins directed against the extra-domain B (ED-B) of oncofetal fibronectin (Fn), a validated marker of tumor neoangiogenesis. The Anticalins were engineered from the human lip ...

    We describe the comparative X-ray structural analysis of three Anticalin proteins directed against the extra-domain B (ED-B) of oncofetal fibronectin (Fn), a validated marker of tumor neoangiogenesis. The Anticalins were engineered from the human lipocalin 2 (Lcn2) scaffold via targeted randomization of the structurally variable loop region and selection by phage display, resulting in 15-19 exchanged residues. While the four reshaped loops exhibit diverse conformations (with shifts in Cα positions up to 20.4 Å), the β-barrel core of the lipocalin remains strongly conserved, thus confirming the extraordinary robustness of this scaffold. All three Anticalins bind the cc' hairpin loop of ED-B, the most exposed motif in the context of its neighboring Fn domains, but reveal entirely different binding modes, with orientations differing by up to 180°. Hence, each Anticalin recognizes its molecular target in an individual manner, in line with the distinct epitope specificities previously seen in binding experiments.


    Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany.,Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany. Electronic address: skerra@tum.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil gelatinase-associated lipocalin
A, C
188Homo sapiensMutation(s): 21 
Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens)
Go to Gene View: LCN2
Go to UniProtKB:  P80188
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibronectin
B, D
106Homo sapiensMutation(s): 0 
Gene Names: FN1 (FN)
Find proteins for P02751 (Homo sapiens)
Go to Gene View: FN1
Go to UniProtKB:  P02751
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.456α = 90.00
b = 67.801β = 90.06
c = 76.806γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Database references
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references