Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A3B3C2D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 258.98 kDa 
• Atom Count: 16955 
• Residue Count: 2243 
• Unique protein chains: 3

6SS6

Structure of arginase-2 in complex with the inhibitory human antigen-binding fragment Fab C0020187

• DOI: 10.2210/pdb6SS6/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Cricetulus griseus
• Mutation(s): No 


• Deposited: 2019-09-06 Released: 2020-06-10 
• Deposition Author(s): Burschowsky, D., Addyman, A., Fiedler, S., Groves, M., Haynes, S., Seewooruthun, C., Carr, M.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.361 
• R-Value Work: 0.300 

Literature

Extensive sequence and structural evolution of Arginase 2 inhibitory antibodies enabled by an unbiased approach to affinity maturation.

Chan, D.T.Y., Jenkinson, L., Haynes, S.W., Austin, M., Diamandakis, A., Burschowsky, D., Seewooruthun, C., Addyman, A., Fiedler, S., Ryman, S., Whitehouse, J., Slater, L.H., Gowans, E., Shibata, Y., Barnard, M., Wilkinson, R.W., Vaughan, T.J., Holt, S.V., Cerundolo, V., Carr, M.D., Groves, M.A.T.

(2020) Proc Natl Acad Sci U S A 117: 16949-16960

• PubMed: 32616569 
• DOI: 10.1073/pnas.1919565117
• Primary Citation of Related Structures:  
  6SS5, 6SS6


• PubMed Abstract: 
  

Affinity maturation is a powerful technique in antibody engineering for the in vitro evolution of antigen binding interactions. Key to the success of this process is the expansion of sequence and combinatorial diversity to increase the structural repertoire from which superior binding variants may be selected. However, conventional strategies are often restrictive and only focus on small regions of the antibody at a time. In this study, we used a method that combined antibody chain shuffling and a staggered-extension process to produce unbiased libraries, which recombined beneficial mutations from all six complementarity-determining regions (CDRs) in the affinity maturation of an inhibitory antibody to Arginase 2 (ARG2). We made use of the vast display capacity of ribosome display to accommodate the sequence space required for the diverse library builds. Further diversity was introduced through pool maturation to optimize seven leads of interest simultaneously. This resulted in antibodies with substantial improvements in binding properties and inhibition potency. The extensive sequence changes resulting from this approach were translated into striking structural changes for parent and affinity-matured antibodies bound to ARG2, with a large reorientation of the binding paratope facilitating increases in contact surface and shape complementarity to the antigen. The considerable gains in therapeutic properties seen from extensive sequence and structural evolution of the parent ARG2 inhibitory antibody clearly illustrate the advantages of the unbiased approach developed, which was key to the identification of high-affinity antibodies with the desired inhibitory potency and specificity.

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Organizational Affiliation: 

Antibody Discovery & Protein Engineering, BioPharmaceuticals Research & Development, AstraZeneca, CB21 6GH Cambridge, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase-2, mitochondrial	AAA, BBB, CCC	346	Homo sapiens	Mutation(s): 0  Gene Names: ARG2 EC: 3.5.3.1
Find proteins for P78540 (Homo sapiens) Explore P78540  Go to UniProtKB:  P78540
NIH Common Fund Data Resources
PHAROS:  P78540 GTEx:  ENSG00000081181

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C0020187 heavy chain (IgG1)	HHH, III, JJJ	233	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab C0020187 light chain (IgG1)	LLL, MMM, NNN	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AAA, BBB, CCC, HHH, III, JJJ, LLL, MMM	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MN	AAA, BBB, CCC	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.361 
• R-Value Work: 0.300 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.126	α = 90
b = 138.126	β = 90
c = 551.307	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-09-06 
• Released Date: 2020-06-10 
Deposition Author(s): Burschowsky, D., Addyman, A., Fiedler, S., Groves, M., Haynes, S., Seewooruthun, C., Carr, M.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C1362/A20263

Revision History 

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2020-07-22
  Changes: Database references
• Version 1.2: 2020-08-05
  Changes: Database references, Derived calculations