PDBsum entry 1fc1

Immunoglobulin

PDB id: 1fc1

Contents

Protein chain

207 a.a. *

Ligands

NAG-NAG-MAN-MAN-NAG-GAL-MAN-NAG-FUC ×2

* Residue conservation analysis

References listed in PDB file

Key reference

• Title: Crystallographic refinement and atomic models of a human fc fragment and its complex with fragment b of protein a from staphylococcus aureus at 2.9- And 2.8-A resolution.
• Author: J.Deisenhofer.
• Ref.: Biochemistry, 1981, 20, 2361-2370. [DOI no: 10.1021/bi00512a001]
• PubMed id: 7236608

Abstract

The model of human Fc fragment was refined at 2.9-A resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sec. B B31, 238; Jack, A., & Levitt, M. (1978) Acta Crystallogr., Sect. A A34, 931]. The final R value is 0.22. The dimer of CH3 domains closely resembles the CH1-CL aggregate in Fab fragments. There is no contact between CH2 domains. The contact between CH2 and CH3 domains has about one-third of the size of the CH3-CH3 contact. The carbohydrate, a branched chain of nine hexose units, covers parts of the C-contact face of the CH2 domain, shielding hydrophobic residues on this surface. Six atoms of the carbohydrate are within hydrogen-bonding distance of atoms in the CH2 domain. Crystallographic refinement of the complex between Fc fragment and fragment B of protein A from Staphylococcus aureus reduced the R value of the model is 0.24. A major part of the structure of fragment B consists of two alpha helics; the rest of the polypeptide chain is folded irregularly. In the crystal, fragment B forms two contacts with Fc fragment molecules. Contact 1 involves residues from both helices of fragment B, and residues from the CH2 and CH3 domains of FC, and is predominantly hydrophobic. Contact 2 is smaller than contact 1. Residues from the second helix and adjacent residues of fragment B and residues only from the CH3 domain of Fc contribute to contact 2. The nature of contact 2 is mainly polar and includes a sulfate ion. There are strong arguments that contact 1 is the fragment B-Fc contact formed in solution under physiological conditions, while contact 2 is a crystal contact.

Secondary reference #1

• Title: Crystallographic structural studies of a human fc fragment. Ii. A complete model based on a fourier map at 3.5 a resolution.
• Authors: J.Deisenhofer, P.M.Colman, O.Epp, R.Huber.
• Ref.: Hoppe Seylers Z Physiol Chem, 1976, 357, 1421-1434.
• PubMed id: 992566

Secondary reference #2

• Title: Crystallographic structural studies of a human fc-Fragment. I. An electron-Density map at 4 a resolution and a partial model.
• Authors: J.Deisenhofer, P.M.Colman, R.Huber, H.Haupt, G.Schwick.
• Ref.: Hoppe Seylers Z Physiol Chem, 1976, 357, 435-445.
• PubMed id: 955567

Secondary reference #3

• Title: X-Ray studies on antibody fragments.
• Authors: P.M.Colman, O.Epp, H.Fehlhammer, W.Bode, M.Schiffer, E.E.Lattman, T.A.Jones, W.Palm.
• Ref.: FEBS Lett, 1974, 44, 194-199. [DOI no: 10.1016/0014-5793(74)80724-6]
• PubMed id: 4138920