5L9D

AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model

Summary for 5L9D

• Entry DOI: 10.2210/pdb5l9d/pdb
• Related: 5L7X 5LGH
• Descriptor: MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA HEAVY CHAIN, MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA LIGHT CHAIN, TETRAETHYLENE GLYCOL, ... (9 entities in total)
• Functional Keywords: afamin antibody, fab fragment, igg1-kappa, light chain glycosilation, immune system
• Biological source: Mus musculus (House Mouse); More
• Total number of polymer chains: 2
• Total formula weight: 48832.32

Authors

Rupp, B.,Naschberger, A. (deposition date: 2016-06-10, release date: 2016-08-03, Last modification date: 2024-11-13)

Primary citation

Naschberger, A.,Furnrohr, B.G.,Lenac Rovis, T.,Malic, S.,Scheffzek, K.,Dieplinger, H.,Rupp, B.
The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.
Acta Crystallogr D Struct Biol, 72:1267-1280, 2016

PubMed Abstract: The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the V1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable V and V domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.

PubMed: 27917827
DOI: 10.1107/S205979831601723X

Experimental method

X-RAY DIFFRACTION (1.88 Å)