6SS6

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 reperto ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase-2, mitochondrial AAABBBCCC346Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C0020187 heavy chain (IgG1) HHHIIIJJJ233Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab C0020187 light chain (IgG1) LLLMMMNNN220Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AAA, BBB, CCC, HHH, III, JJJ, LLL, MMM
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
AAA, BBB, CCC
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
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 = 138.126α = 90
b = 138.126β = 90
c = 551.307γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC1362/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