Crystal structure of human CD59

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

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Crystal structure of CD59: implications for molecular recognition of the complement proteins C8 and C9 in the membrane-attack complex.

Huang, Y.Fedarovich, A.Tomlinson, S.Davies, C.

(2007) Acta Crystallogr D Biol Crystallogr 63: 714-721

  • DOI: https://doi.org/10.1107/S0907444907015557
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human CD59 is a small membrane-bound glycoprotein that functions as an inhibitor of the membrane-attack complex (MAC) of the complement system by binding the complement proteins C8 and C9. The crystal structure of a soluble construct of CD59 has been determined to 2.1 A resolution. When compared with previous models of CD59 determined using NMR, some interesting differences are noted, including the position of helix alpha1, which contributes to the binding surface for C8 and C9. Interestingly, the crystal structure superimposes more closely with an updated NMR model of CD59 that was produced using Monte Carlo minimization, including helix alpha1. Mapping of mutations associated with enhanced or lowered inhibitory function of CD59 show the binding region to be located in a crevice between alpha1 and a three-stranded beta-sheet, as has been identified previously. Residues in the core of this region are well ordered in the electron density, in part owing to a network of stabilizing covalent and noncovalent interactions, and manifest an interesting 'striped' distribution of hydrophobic and basic residues. Docking of the same peptide that was modeled previously into the NMR structure shows that Arg55, which has been postulated to exist in 'open' and 'closed' positions, is intermediate in position between these two and is well placed to contact the peptide. Further clues regarding how CD59 interacts with small peptides arise from the crystal packing of this structure, which shows that a symmetry-related loop comprising residues 20-24 occupies a spatially similar position to the modeled peptide. This higher resolution structure of CD59 will facilitate a more precise dissection of its interactions with C8 and C9 and thus increase the likelihood of designing enhanced CD59-based therapeutics.

  • Organizational Affiliation

    Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CD59 glycoprotein75Homo sapiensMutation(s): 1 
Gene Names: CD59
UniProt & NIH Common Fund Data Resources
Find proteins for P13987 (Homo sapiens)
Explore P13987 
Go to UniProtKB:  P13987
PHAROS:  P13987
GTEx:  ENSG00000085063 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13987
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.4α = 90
b = 56.4β = 90
c = 39.4γ = 120
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2007-05-29 
  • Deposition Author(s): Davies, C.

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2021-10-20
    Changes: Database references
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description