5U4Y

IgG Fc bound to 3 helix of the B-domain from Protein A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4994 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

3-2-1: Structural insights from stepwise shrinkage of a three-helix Fc-binding domain to a single helix.

Ultsch, M.Braisted, A.Maun, H.R.Eigenbrot, C.

(2017) Protein Eng. Des. Sel. 30: 619-625

  • DOI: 10.1093/protein/gzx029
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The well-studied B-domain from Staphylococcal protein A is a 59 amino acid three-helix bundle that binds the Fc portion of IgG with a dissociation constant of ~35 nM. The B-domain variant bearing a Gly to Ala mutation (=Z-domain) has been the subject ...

    The well-studied B-domain from Staphylococcal protein A is a 59 amino acid three-helix bundle that binds the Fc portion of IgG with a dissociation constant of ~35 nM. The B-domain variant bearing a Gly to Ala mutation (=Z-domain) has been the subject of efforts to minimize a domain's size while retaining its function. We report X-ray crystallographic characterization of three steps in such a process using complexes with Fc: the full three-helix Z-domain, a 34 amino acid two-helix version called Z34C and a 13 amino acid single helix stabilized with an exo-helix tether, called LH1.


    Related Citations: 
    • 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.
      Deisenhofer, J.
      (1981) Biochemistry 20: 2361


    Organizational Affiliation

    Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080,USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG1 fc
A, B
212Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin G-binding protein A
C, D
55Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Gene Names: spa
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  P02976
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4994 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.950α = 90.00
b = 152.260β = 90.00
c = 46.600γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references