PDBsum entry: 1fc2

Immunoglobulin

PDB-id: 1fc2

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

44 a.a. *

207 a.a. *

Ligands

NAG-FUC-NAG-MAN-MAN-NAG-GAL-MAN-NAG

SO4

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1fc2

Name:

Immunoglobulin

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-angstroms resolution

Structure:

Fragment b of protein a complex. Chain: c. Engineered: yes. Immunoglobulin fc. Chain: d. Engineered: yes

Source:

Staphylococcus aureus subsp. Aureus nctc 8325. Organism_taxid: 93061. Strain: nctc 8325. Homo sapiens. Human. Organism_taxid: 9606

Biological unit:

Dimer (from PQS)

UniProt:

Chain C: P02976 (SPA1_STAA8)

Seq:

Struc:

Seq:

516 a.a.

Struc:

44 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.80Å

R-factor:

not given

Authors:

J.Deisenhofer

Key ref:

J.Deisenhofer (1981). 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.. Biochemistry, 20, 2361-2370. [PubMed id: 7236608] [DOI: 10.1021/bi00512a001]

Date:

21-May-81

Release date:

02-Oct-81

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1021/bi00512a001

Biochemistry 20:2361-2370 (1981)

PubMed id: 7236608

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.

J.Deisenhofer.

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.