PDBsum entry 2jb5

Immune system

PDB id: 2jb5

Contents

Protein chains

217 a.a. *

212 a.a. *

Ligands

T5C

Waters ×47

* Residue conservation analysis

PDB id:

2jb5

Name:

Immune system

Title:

Fab fragment in complex with small molecule hapten, crystal form-1

Structure:

Fab fragment mor03268 heavy chain. Chain: h. Engineered: yes. Fab fragment mor03268 light chain. Chain: l. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: in vitro selected from a library and optimized in several maturation steps. Several maturation steps

Resolution:

2.80Å R-factor: 0.211 R-free: 0.272

Authors:

R.C.Hillig,S.Baesler,G.Malawski,V.Badock,I.Bahr,M.Schirner,K.Licha

Key ref:

R.C.Hillig et al. (2008). Fab MOR03268 triggers absorption shift of a diagnostic dye via packaging in a solvent-shielded Fab dimer interface. J Mol Biol, 377, 206-219. PubMed id: 18241888 DOI: 10.1016/j.jmb.2007.12.071

Date:

03-Dec-06 Release date: 08-Jan-08

Protein chain

No UniProt id for this chain

Struc: 217 a.a.

Protein chain

P0DOY2  (IGLC2_HUMAN) -  Immunoglobulin lambda constant 2 from Homo sapiens

Seq: 106 a.a.

Struc: 212 a.a.

DOI no: 10.1016/j.jmb.2007.12.071

J Mol Biol 377:206-219 (2008)

PubMed id: 18241888

Fab MOR03268 triggers absorption shift of a diagnostic dye via packaging in a solvent-shielded Fab dimer interface.

R.C.Hillig, S.Urlinger, J.Fanghänel, B.Brocks, C.Haenel, Y.Stark, D.Sülzle, D.I.Svergun, S.Baesler, G.Malawski, D.Moosmayer, A.Menrad, M.Schirner, K.Licha.

ABSTRACT

Molecular interactions between near-IR fluorescent probes and specific antibodies may be exploited to generate novel smart probes for diagnostic imaging. Using a new phage display technology, we developed such antibody Fab fragments with subnanomolar binding affinity for tetrasulfocyanine, a near-IR in vivo imaging agent. Unexpectedly, some Fabs induced redshifts of the dye absorption peak of up to 44 nm. This is the largest shift reported for a biological system so far. Crystal structure determination and absorption spectroscopy in the crystal in combination with microcalorimetry and small-angle X-ray scattering in solution revealed that the redshift is triggered by formation of a Fab dimer, with tetrasulfocyanine being buried in a fully closed protein cavity within the dimer interface. The derived principle of shifting the absorption peak of a symmetric dye via packaging within a Fab dimer interface may be transferred to other diagnostic fluorophores, opening the way towards smart imaging probes that change their wavelength upon interaction with an antibody.

Selected figure(s)

Figure 4.
Fig. 4. Crystal structures of the complex of Fab MOR03268:TSC in two crystal forms. (a) Overall view of the 1:1 complex in crystal form 1. The Fab molecule is shown in secondary structure and surface representation, with the heavy chain depicted in blue and the light chain in orange. TSC (stick representation) is bound within a deep surface cavity in the antigen-binding site located at the interface between the two N-terminal variable immunoglobulin domains (V[L] and V[H]). C[H] and C[L] refer to the constant immunoglobulin domains of the heavy and light chain. (b) Stereo representation showing the detailed binding mode of TSC in form 1. Both the light chain (orange) and the heavy chain (blue) contribute three loops, the complementarity determining regions (CDRs). (c) Overall view of the 2:1 complex in crystal form 2. TSC is bound in the interface between two Fab molecules, resulting in a TSC-induced Fab dimer with a very elongated molecular shape. The zoom on the right side shows a cross section through the Fab dimer interface, illustrating that the bound TSC molecule site is fully shielded from the solvent.

Figure 5.
Fig. 5. SAXS experiments and ab initio SAXS models. (a) Processed experimental SAXS data (dots with error bars, labeled from top to bottom): (1) Fab MOR03268, an equimolar Fab–TSC mixture, a mixture with 1:10 excess of TSC, and the scattering calculated from the models; (2) monomeric Fab crystal form 1; (3) compact side-by-side crystallographic Fab dimer observed in the crystal packing of form 2; (4) elongated Fab dimer from crystal form 2; (5) a mixture of form 1 and the elongated dimer from form 2. The plot displays the logarithm of the scattering intensity I versus momentum transfer s = 4π sin θ/λ, where 2θ is the scattering angle and λ = 1.5 Å is the X-ray wavelength. The curves are displaced along the abscissa for clarity. (b) Ab initio SAXS models derived from the data of TSC-free Fab and of the equimolar Fab–TSC mixture (semitransparent beads) superimposed with the monomeric crystal form 1 and the elongated Fab dimer from form 2 (left and right panels, respectively). Three orthogonal views are displayed.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 377, 206-219) copyright 2008.

Figures were selected by an automated process.