Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B2C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 131.44 kDa 
• Atom Count: 8431 
• Modelled Residue Count: 1103 
• Deposited Residue Count: 1150 
• Unique protein chains: 3

6PPG

Crystal structure of IL17FF bound to Fab fragments of MCAF5352A

• PDB DOI: 10.2210/pdb6PPG/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2019-07-06 Released: 2019-12-11 
• Deposition Author(s): Huang, C.S., Yin, J.P., Hymowitz, S.G.

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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 

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

• PubMed: 31779513 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-17F	A [auth F], F [auth G]	133	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MCAF5352A light chain	B [auth A], E [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab MCAF5352A heavy chain	C [auth B], D [auth H]	226	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	CB [auth G], G [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD	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

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 = 103.82	α = 90
b = 103.82	β = 90
c = 243.327	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-07-06 
• Released Date: 2019-12-11 
Deposition Author(s): Huang, C.S., Yin, J.P., Hymowitz, S.G.

Revision History  

• 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