The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in two crystal forms at 2.2 and 2.9 Å resolution

Fokin, A. V.; Afonin, P.V.; Mikhailova, I. Yu.; Tsygannik, I.N.; Mareeva, T. Yu.; Nesmeyanov, V. A.; Pangborn, W.; Lee, N.; Duax, William L.; Ciszak, Ewa; Плетнев, В. З.

doi:10.1007/bf02758622

Cited by 9 publications

(9 citation statements)

References 15 publications

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“…The structure was solved by the molecular replacement (MR) method using ClfA CC (pdbid; 1VR3) as the search model. To determine the MR solution for the Fab fragment, several poly-alanine models of Fv fragments from the PDB database were attempted of which pdb id; 1F8T (Fokin et al, 2000) yielded a reasonable MR solution. The model was rebuilt using Coot (Emsley and Cowtan, 2004) and refined using PHENIX (Adams et al, 2002) and Refmac 5.0 (Murshudov et al, 1997) to a final R-factor of 0.207 and an R free of 0.259.…”

Section: Methodsmentioning

confidence: 99%

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody

Ganesh¹,

Liang²,

Geoghegan

et al. 2016

EBioMedicine

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The Staphylococcus aureus fibrinogen binding MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules), ClfA (clumping factor A) is an important virulence factor in staphylococcal infections and a component of several vaccines currently under clinical evaluation. The mouse monoclonal antibody aurexis (also called 12-9), and the humanized version tefibazumab are therapeutic monoclonal antibodies targeting ClfA that in combination with conventional antibiotics were effective in animal models but showed less impressive efficacy in a limited Phase II clinical trial. We here report the crystal structure and a biochemical characterization of the ClfA/tefibazumab (Fab) complex. The epitope for tefibazumab is located to the “top” of the N3 subdomain of ClfA and partially overlaps with a previously unidentified second binding site for fibrinogen. A high-affinity binding of ClfA to fibrinogen involves both an interaction at the N3 site and the previously identified docking of the C-terminal segment of the fibrinogen γ-chain in the N2N3 trench. Although tefibazumab binds ClfA with high affinity we observe a modest IC50 value for the inhibition of fibrinogen binding to the MSCRAMM. This observation, paired with a common natural occurring variant of ClfA that is not effectively recognized by the mAb, may partly explain the modest effect tefibazumab showed in the initial clinic trail. This information will provide guidance for the design of the next generation of therapeutic anti-staphylococcal mAbs targeting ClfA.

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Section: Methodsmentioning

confidence: 99%

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody

Ganesh¹,

Liang²,

Geoghegan

et al. 2016

EBioMedicine

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“…The re®nement tests were carried out with CNS complex (Bru È nger et al, 1998) using the structure of the Fab fragment of the monoclonal antibody (Fokine et al, 2000). The full model included 439 amino acid residues and 213 water molecules.…”

Section: Numerical Testsmentioning

confidence: 99%

Likelihood-based refinement. I. Irremovable model errors

Lunin

Afonine

Urzhumtsev

2002

Acta Crystallogr A Found Crystallogr

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In conventional structure re®nement, the discrepancy between the calculated magnitudes and those observed in X-ray experiments is attributed to errors inherent in preliminary assigned values of the model parameters. However, the chosen set of model parameters may not be adequate to describe the structure factors precisely. For example, if some atoms are not included in the current model, then the structure factors calculated from such a partial model contaiǹ irremovable errors'. These errors cannot be eliminated by any choice of the parameters of the partial structure. Probabilistic modelling suggests a way to take irremovable errors into account. Every trial set of values of the model parameters is now associated with the joint probability distribution of the calculated magnitudes, rather than with a particular set of magnitudes. The new goal of the re®nement is formulated as the search for the distribution that is the most consistent with the observed data. The statistical likelihood is a possible measure of the consistency. The suggested quadratic approximation of the likelihood function allows the likelihood-based re®nement to be considered as a kind of least-squares re®nement that uses appropriate weights and modi®ed targets for the calculated magnitudes. This in turn enables the analysis of tendencies of the likelihood-based re®nement in comparison with the classical least-squares re®nement.

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“…The overall conformation of the Fab-LNKB-2 antibody is similar in the uncomplexed (Fokin et al 2000) and complexed structures with a root mean square deviation (RMSD) of 0.55 Å for 425 of the total 439 C ␣ atoms. Those excluded because of weak electron density are identified in the Materials and Methods section.…”

Section: Overall Structurementioning

confidence: 99%

“…The structure of the Fab-peptide complex was determined by the molecular replacement technique with the software package AMoRe (Navaza 1994) using the unliganded Fab crystal structure in P2 1 2 1 2 1 space group (Fokin et al 2000) as a search probe and a 3.5 to 10.0-Å data shell. The solution was indicated unequivocally by the correlation coefficient (C-factor) and R-factor magnitudes of 74.1 and 30.0, respectively.…”

Section: Structure Determination and Crystallographic Refinementmentioning

confidence: 99%

“…Our determination of the 2.2-Å resolution crystal structure of the unliganded Fab of LNKB-2 provided detailed information concerning the antibody binding site (Fokin et al 2000). In this paper we present the results of an X-ray study of the crystal structure of Fab-LNKB-2 in complex with the antigenic nonapeptide Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-OMe, an analog of the IL-2 epitope fragment 64-72.…”

mentioning

confidence: 99%

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Crystal structure of an anti‐interleukin‐2 monoclonal antibody Fab complexed with an antigenic nonapeptide

et al. 2001

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The three-dimensional structure of the Fab fragment of a monoclonal antibody (LNKB-2) to human interleukin-2 (IL-2) complexed with a synthetic antigenic nonapeptide, Ac-Lys-Pro-Leu-Glu-Glu-Val-Leu-AsnLeu-OMe, has been determined at 3.0 Å resolution. In the structure, four out of the six hypervariable loops of the Fab (complementarity determining regions [CDRs] L1, H1, H2, and H3) are involved in peptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. The Tyr residues in the Fab antigen binding site play a major role in antigen-antibody recognition. The structures of the complexed and uncomplexed Fab were compared. In the antigen binding site the CDR-L1 loop of the antibody shows the largest structural changes upon peptide binding. The peptide adopts a mostly ␣-helical conformation similar to that in the epitope fragment 64-72 of the IL-2 antigen. The side chains of residues Leu 66, Val 69, and Leu 70, which are shielded internally in the IL-2 structure, are involved in interactions with the Fab in the complex studied. This indicates that antibody-antigen complexation involves a significant rearrangement of the epitope-containing region of the IL-2 with retention of the ␣-helical character of the epitope fragment.Keywords: Monoclonal antibody; Fab-antigen binding fragment; interleukin-2 antigen; antibody-antigen interaction; three-dimensional structure; X-ray analysis Monoclonal antibodies are used widely in biomedical research because of their stereochemical complementarity to specific antigens. Determination of the structural basis of antibody-antigen specificity is important to understanding the mechanism of immune recognition and the rational design of pharmacological agents, synthetic vaccines, and antibodies with novel selectivities. Some aspects of the recognition process remain unclear. The determination of the X-ray crystal structures of a number of unliganded antibodies, isolated antigens, and their complexes has advanced understanding of the nature of antibody-protein-antigen interactions (see selected references:

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The three-dimensional structure of the antigen-binding fragment of a monoclonal antibody to human interleukin-2 in two crystal forms at 2.2 and 2.9 Å resolution

Cited by 9 publications

References 15 publications

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody

Lessons from the Crystal Structure of the S. aureus Surface Protein Clumping Factor A in Complex With Tefibazumab, an Inhibiting Monoclonal Antibody

Likelihood-based refinement. I. Irremovable model errors

Crystal structure of an anti‐interleukin‐2 monoclonal antibody Fab complexed with an antigenic nonapeptide

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