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-Å resolution

Research output: Contribution to journalArticle

1242 Citations (Scopus)

Abstract

The model of human Fc fragment was refined at 2.9-Å resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sect. 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 part 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 to 0.24. A major part of the structure of fragment B consists of two α helices; 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.

Original languageEnglish (US)
Pages (from-to)2361-2370
Number of pages10
JournalBiochemistry
Volume20
Issue number9
StatePublished - 1981

Fingerprint

Immunoglobulin Fc Fragments
Staphylococcal Protein A
Staphylococcus aureus
Contacts (fluid mechanics)
Carbohydrates
Atoms
Immunoglobulin Fab Fragments
Crystals
Jacks
Hexoses
Dimers
Shielding
Sulfates
Hydrogen bonds
Hydrogen Bonding
Ions
Peptides
Molecules

ASJC Scopus subject areas

  • Biochemistry

Cite this

@article{c6af0b9c779441c19b13bd3f56615275,
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-{\AA} resolution",
abstract = "The model of human Fc fragment was refined at 2.9-{\AA} resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sect. 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 part 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 to 0.24. A major part of the structure of fragment B consists of two α helices; 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.",
author = "Johann Deisenhofer",
year = "1981",
language = "English (US)",
volume = "20",
pages = "2361--2370",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "9",

}

TY - JOUR

T1 - 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-Å resolution

AU - Deisenhofer, Johann

PY - 1981

Y1 - 1981

N2 - The model of human Fc fragment was refined at 2.9-Å resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sect. 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 part 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 to 0.24. A major part of the structure of fragment B consists of two α helices; 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.

AB - The model of human Fc fragment was refined at 2.9-Å resolution. Two different automated procedures for crystallographic refinement were used [Deisenhofer, J., & Steigemann, W. (1975) Acta Crystallogr., Sect. 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 part 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 to 0.24. A major part of the structure of fragment B consists of two α helices; 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.

UR - http://www.scopus.com/inward/record.url?scp=0019522383&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0019522383&partnerID=8YFLogxK

M3 - Article

VL - 20

SP - 2361

EP - 2370

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 9

ER -