4EOW

Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular structure of human GM-CSF in complex with a disease-associated anti-human GM-CSF autoantibody and its potential biological implications.

Blech, M.Seeliger, D.Kistler, B.Bauer, M.M.Hafner, M.Horer, S.Zeeb, M.Nar, H.Park, J.E.

(2012) Biochem.J. 447: 205-215

  • DOI: 10.1042/BJ20120884

  • PubMed Abstract: 
  • Polyclonal autoantibodies against human GM-CSF (granulocyte/macrophage colony-stimulating factor) are a hallmark of PAP (pulmonary alveolar proteinosis) and several other reported autoimmune diseases. MB007 is a high-affinity anti-(human GM-CSF) auto ...

    Polyclonal autoantibodies against human GM-CSF (granulocyte/macrophage colony-stimulating factor) are a hallmark of PAP (pulmonary alveolar proteinosis) and several other reported autoimmune diseases. MB007 is a high-affinity anti-(human GM-CSF) autoantibody isolated from a patient suffering from PAP which shows only modest neutralization of GM-CSF bioactivity. We describe the first crystal structure of a cytokine-directed human IgG1λ autoantibody-binding fragment (Fab) at 1.9 Å (1 Å=0.1 nm) resolution. Its CDR3-H substantially differs from all VH7 germline IgG1 structures reported previously. We derive a reliable model of the antigen-autoantibody complex by using NMR chemical shift perturbation data in combination with computational methods. Superposition of the modelled complex structure with the human GM-CSF-GM-CSF ternary receptor complex reveals only little overlap between receptor and Fab when bound to GM-CSF. Our model provides a structural basis for understanding the mode of action of the MB007 autoantibody.


    Organizational Affiliation

    Department of Lead Identification and Optimization Support, Structural Research Group, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, 88397 Biberach, Germany. michaela.blech@boehringer-ingelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MB007 human IgG1 Fab fragment heavy chain
H
228Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MB007 IgG1 Fab fragment light chain
L
216Homo sapiensMutation(s): 0 
Gene Names: IGLC3
Find proteins for P0DOY3 (Homo sapiens)
Go to UniProtKB:  P0DOY3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.289α = 90.00
b = 47.786β = 90.00
c = 159.244γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
AutoPROCdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-16 
  • Released Date: 2012-08-22 
  • Deposition Author(s): Blech, M.

Revision History 

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references
  • Version 1.2: 2012-10-10
    Type: Database references
  • Version 1.3: 2017-06-28
    Type: Database references, Source and taxonomy, Structure summary