5F3B

Structure of myostatin in complex with chimeric RK35 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Beyond CDR-grafting: Structure-guided humanization of framework and CDR regions of an anti-myostatin antibody.

Apgar, J.R.Mader, M.Agostinelli, R.Benard, S.Bialek, P.Johnson, M.Gao, Y.Krebs, M.Owens, J.Parris, K.St Andre, M.Svenson, K.Morris, C.Tchistiakova, L.

(2016) Mabs 8: 1302-1318

  • DOI: 10.1080/19420862.2016.1215786
  • Primary Citation of Related Structures:  5F3H

  • PubMed Abstract: 
  • Antibodies are an important class of biotherapeutics that offer specificity to their antigen, long half-life, effector function interaction and good manufacturability. The immunogenicity of non-human-derived antibodies, which can be a major limitatio ...

    Antibodies are an important class of biotherapeutics that offer specificity to their antigen, long half-life, effector function interaction and good manufacturability. The immunogenicity of non-human-derived antibodies, which can be a major limitation to development, has been partially overcome by humanization through complementarity-determining region (CDR) grafting onto human acceptor frameworks. The retention of foreign content in the CDR regions, however, is still a potential immunogenic liability. Here, we describe the humanization of an anti-myostatin antibody utilizing a 2-step process of traditional CDR-grafting onto a human acceptor framework, followed by a structure-guided approach to further reduce the murine content of CDR-grafted antibodies. To accomplish this, we solved the co-crystal structures of myostatin with the chimeric (Protein Databank (PDB) id 5F3B) and CDR-grafted anti-myostatin antibody (PDB id 5F3H), allowing us to computationally predict the structurally important CDR residues as well as those making significant contacts with the antigen. Structure-based rational design enabled further germlining of the CDR-grafted antibody, reducing the murine content of the antibody without affecting antigen binding. The overall "humanness" was increased for both the light and heavy chain variable regions.


    Organizational Affiliation

    a Biomedicine Design, Pfizer Inc. , Cambridge , MA , USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RK35 Chimeric antibody heavy chain
A, E
221N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RK35 Chimeric antibody light chain
B, F
213N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Growth/differentiation factor 8
C, D
109Homo sapiensGene Names: MSTN (GDF8)
Find proteins for O14793 (Homo sapiens)
Go to Gene View: MSTN
Go to UniProtKB:  O14793
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.090α = 78.98
b = 67.616β = 88.77
c = 78.559γ = 67.44
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
AMoREphasing
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references