5XHG | pdb_00005xhg

Crystal structure of Trastuzumab Fab fragment bearing Ne-(o-azidobenzyloxycarbonyl)-L-lysine

• PDB DOI: https://doi.org/10.2210/pdb5XHG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 2017-04-20 Released: 2017-12-20 
• Deposition Author(s): Kuratani, M., Yanagisawa, T., Sakamoto, K., Yokoyama, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Extensive Survey of Antibody Invariant Positions for Efficient Chemical Conjugation Using Expanded Genetic Codes.

Kato, A., Kuratani, M., Yanagisawa, T., Ohtake, K., Hayashi, A., Amano, Y., Kimura, K., Yokoyama, S., Sakamoto, K., Shiraishi, Y.

(2017) Bioconjug Chem 28: 2099-2108

• PubMed: 28727448 
• DOI: https://doi.org/10.1021/acs.bioconjchem.7b00265
• Primary Citation Related Structures: 
  5XHF, 5XHG


• PubMed Abstract: 
  

  The site-specific chemical conjugation of proteins, following synthesis with an expanded genetic code, promises to advance antibody-based technologies, including antibody drug conjugation and the creation of bispecific Fab dimers. The incorporation of non-natural amino acids into antibodies not only guarantees site specificity but also allows the use of bio-orthogonal chemistry. However, the efficiency of amino acid incorporation fluctuates significantly among different sites, thereby hampering the identification of useful conjugation sites. In this study, we applied the codon reassignment technology to achieve the robust and efficient synthesis of chemically functionalized antibodies containing N ^ε -(o-azidobenzyloxycarbonyl)-l-lysine (o-Az-Z-Lys) at defined positions. This lysine derivative has a bio-orthogonally reactive group at the end of a long side chain, enabling identification of multiple new positions in Fab-constant domains, allowing chemical conjugation with high efficiency. An X-ray crystallographic study of a Fab variant with o-Az-Z-Lys revealed high-level exposure of the azido group to solvent, with six of the identified positions subsequently used to engineer "Variabodies", a novel antibody format allowing various connections between two Fab molecules. Our findings indicated that some of the created Variabodies exhibited agonistic activity in cultured cells as opposed to the antagonistic nature of antibodies. These results showed that our approach greatly enhanced the availability of antibodies for chemical conjugation and might aid in the development of new therapeutic antibodies.

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Organizational Affiliation: 
• RIKEN Structural Biology Laboratory , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
RIKEN Systems and Structural Biology Center , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.04 kDa 
• Atom Count: 7,919 
• Modeled Residue Count: 861 
• Deposited Residue Count: 868 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
polypeptide(L)	A, C	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
polypeptide(H)	B, D	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAZ	E [auth A]	(2-azidophenyl)methyl hydrogen carbonate C8 H7 N3 O2 YHJYQHHCLBKKKY-UHFFFAOYSA-N
PEG	I [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth A], J [auth C], P [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth A], H [auth B], K [auth C], L [auth C], M [auth C], N [auth C], Q [auth D], R [auth D], S [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.651	α = 113.5
b = 79.891	β = 92.82
c = 85.764	γ = 102.84

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Kuratani, M., Yanagisawa, T., Sakamoto, K., Yokoyama, S.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-25
  Changes: Source and taxonomy
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary