6PPG

Crystal structure of IL17FF bound to Fab fragments of MCAF5352A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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This is version 1.1 of the entry. See complete history


Literature

Dissecting the molecular basis of high viscosity of monospecific and bispecific IgG antibodies.

Tilegenova, C.Izadi, S.Yin, J.Huang, C.S.Wu, J.Ellerman, D.Hymowitz, S.G.Walters, B.Salisbury, C.Carter, P.J.

(null) MAbs 12: 1692764-1692764

  • DOI: 10.1080/19420862.2019.1692764
  • Primary Citation of Related Structures:  
    6PPG

  • PubMed Abstract: 
  • Some antibodies exhibit elevated viscosity at high concentrations, making them poorly suited for therapeutic applications requiring administration by injection such as subcutaneous or ocular delivery. Here we studied an anti-IL-13/IL-17 bispecific IgG 4 antibody, which has anomalously high viscosity compared to its parent monospecific antibodies ...

    Some antibodies exhibit elevated viscosity at high concentrations, making them poorly suited for therapeutic applications requiring administration by injection such as subcutaneous or ocular delivery. Here we studied an anti-IL-13/IL-17 bispecific IgG 4 antibody, which has anomalously high viscosity compared to its parent monospecific antibodies. The viscosity of the bispecific IgG 4 in solution was decreased by only ~30% in the presence of NaCl, suggesting electrostatic interactions are insufficient to fully explain the drivers of viscosity. Intriguingly, addition of arginine-HCl reduced the viscosity of the bispecific IgG 4 by ~50% to its parent IgG level. These data suggest that beyond electrostatics, additional types of interactions such as cation-π and/or π-π may contribute to high viscosity more significantly than previously understood. Molecular dynamics simulations of antibody fragments in the mixed solution of free arginine and explicit water were conducted to identify hotspots involved in self-interactions. Exposed surface aromatic amino acids displayed an increased number of contacts with arginine. Mutagenesis of the majority of aromatic residues pinpointed by molecular dynamics simulations effectively decreased the solution's viscosity when tested experimentally. This mutational method to reduce the viscosity of a bispecific antibody was extended to a monospecific anti-GCGR IgG 1 antibody with elevated viscosity. In all cases, point mutants were readily identified that both reduced viscosity and retained antigen-binding affinity. These studies demonstrate a new approach to mitigate high viscosity of some antibodies by mutagenesis of surface-exposed aromatic residues on complementarity-determining regions that may facilitate some clinical applications.


    Organizational Affiliation

    Antibody Engineering, Genentech Inc., South San Francisco, CA, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-17FA [auth F],
F [auth G]
133Homo sapiensMutation(s): 0 
Gene Names: IL17F
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PD4 (Homo sapiens)
Explore Q96PD4 
Go to UniProtKB:  Q96PD4
PHAROS:  Q96PD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PD4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab MCAF5352A light chainB [auth A],
E [auth L]
216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab MCAF5352A heavy chainC [auth B],
D [auth H]
226Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CB [auth G],
G [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth L],
BA [auth A],
BB [auth L],
CA [auth B],
AA [auth A],
AB [auth L],
BA [auth A],
BB [auth L],
CA [auth B],
DA [auth B],
DB [auth G],
EA [auth B],
EB [auth G],
FA [auth B],
FB [auth G],
GA [auth B],
GB [auth G],
H [auth F],
HA [auth B],
HB [auth G],
I [auth F],
IA [auth B],
IB [auth G],
J [auth F],
JA [auth H],
K [auth F],
KA [auth H],
L [auth F],
LA [auth H],
M [auth A],
MA [auth H],
N [auth A],
NA [auth H],
O [auth A],
OA [auth H],
P [auth A],
PA [auth L],
Q [auth A],
QA [auth L],
R [auth A],
RA [auth L],
S [auth A],
SA [auth L],
T [auth A],
TA [auth L],
U [auth A],
UA [auth L],
V [auth A],
VA [auth L],
W [auth A],
WA [auth L],
X [auth A],
XA [auth L],
Y [auth A],
YA [auth L],
Z [auth A],
ZA [auth L]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.82α = 90
b = 103.82β = 90
c = 243.327γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-11
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary