6GFE

High-resolution Structure of a therapeutic full-length anti-NPRA Antibody with exceptional Conformational Diversity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity.

Blech, M.Horer, S.Kuhn, A.B.Kube, S.Goddeke, H.Kiefer, H.Zang, Y.Alber, Y.Kast, S.M.Westermann, M.Tully, M.D.Schafer, L.V.Garidel, P.

(2019) Biophys.J. 116: 1637-1649

  • DOI: 10.1016/j.bpj.2019.03.036

  • PubMed Abstract: 
  • We report the x-ray crystal structure of intact, full-length human immunoglobulin (IgG4) at 1.8 Å resolution. The data for IgG4 (S228P), an antibody targeting the natriuretic peptide receptor A, show a previously unrecognized type of Fab-Fc orientati ...

    We report the x-ray crystal structure of intact, full-length human immunoglobulin (IgG4) at 1.8 Å resolution. The data for IgG4 (S228P), an antibody targeting the natriuretic peptide receptor A, show a previously unrecognized type of Fab-Fc orientation with a distorted λ-shape in which one Fab-arm is oriented toward the Fc portion. Detailed structural analysis by x-ray crystallography and molecular simulations suggest that this is one of several conformations coexisting in a dynamic equilibrium state. These results were confirmed by small angle x-ray scattering in solution. Furthermore, electron microscopy supported these findings by preserving molecule classes of different conformations. This study fosters our understanding of IgG4 in particular and our appreciation of antibody flexibility in general. Moreover, we give insights into potential biological implications, specifically for the interaction of human anti-natriuretic peptide receptor A IgG4 with the neonatal Fc receptor, Fcγ receptors, and complement-activating C1q by considering conformational flexibility.


    Organizational Affiliation

    Physikalische Chemie III, Technische Universität Dortmund, Dortmund, Germany.,Elektronenmikroskopisches Zentrum, Friedrich-Schiller-Universität Jena, Jena, Germany.,European Synchrotron Radiation Facility, Grenoble, France.,Theoretical Chemistry, Ruhr University Bochum, Bochum, Germany.,Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany.,Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany. Electronic address: patrick.garidel@boehringer-ingelheim.com.,University of Applied Sciences Biberach, Biberach (Riss), Germany.,Innovation Unit, Pharmaceutical Development Biologics, Biberach (Riss), Germany. Electronic address: michaela.blech@boehringer-ingelheim.com.,Department Lead Identification and Optimization Support, Structural Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach (Riss), Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-4 heavy chain
H, K
450N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-4 light chain
L, M
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
K, L
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
H, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
H, K
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
H, K
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
H, K
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
H, K
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.780α = 90.00
b = 160.510β = 110.72
c = 87.300γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-04-30 
  • Released Date: 2019-05-15 
  • Deposition Author(s): Hoerer, S.

Revision History 

  • Version 1.0: 2019-05-15
    Type: Initial release