Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

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Structure at 1.44 A resolution of an N-terminally truncated form of the rat serum complement C3d fragment.

Zanotti, G.Bassetto, A.Battistutta, R.Folli, C.Arcidiaco, P.Stoppini, M.Berni, R.

(2000) Biochim Biophys Acta 1478: 232-238

  • DOI: https://doi.org/10.1016/s0167-4838(00)00040-6
  • Primary Citation of Related Structures:  
    1QQF, 1QSJ

  • PubMed Abstract: 

    Complement component C3 plays a key role in the complement-mediated immune defence, and occupies a central position within the complement cascade system. One of its degradation products, C3dg, was purified from rat serum and crystallised in two different crystal forms as N-terminally truncated fragment. Despite the truncation and the lack of a significant portion of the N-terminus as compared to C3d, the structure of the fragment is highly similar to that of recombinant human C3d (Nagar et al., Science 280 (1998) 1277-1281). Structural details of the reactive site have been obtained, suggesting a possible mode of thioester bond formation between Cys-1010 and Gln-1013 and thioester bond cleavage in the transacylation reaction involving His-1126. The truncation at the N-terminus of C3d leads to the exposure of a surface of the molecule that favours dimerisation, so that in both crystal forms, the fragment is present as a dimer, with monomers related by a two-fold axis.

  • Organizational Affiliation

    Department of Organic Chemistry and Biopolymer Research Center, University of Padova, Italy. zanotti@chor.unipd.it

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
277Rattus norvegicusMutation(s): 3 
Gene Names: C3
Find proteins for P01026 (Rattus norvegicus)
Explore P01026 
Go to UniProtKB:  P01026
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01026
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.62α = 90
b = 99.93β = 90
c = 114.88γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-07-31
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references