Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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This is version 2.0 of the entry. See complete history


Alternative structural state of transferrin. The crystallographic analysis of iron-loaded but domain-opened ovotransferrin N-lobe.

Mizutani, K.Yamashita, H.Kurokawa, H.Mikami, B.Hirose, M.

(1999) J Biol Chem 274: 10190-10194

  • DOI: https://doi.org/10.1074/jbc.274.15.10190
  • Primary Citation of Related Structures:  
    1NFT, 1TFA

  • PubMed Abstract: 

    Transferrins bind Fe3+ very tightly in a closed interdomain cleft by the coordination of four protein ligands (Asp60, Tyr92, Tyr191, and His250 in ovotransferrin N-lobe) and of a synergistic anion, physiologically bidentate CO32-. Upon Fe3+ uptake, transferrins undergo a large scale conformational transition: the apo structure with an opening of the interdomain cleft is transformed into the closed holo structure, implying initial Fe3+ binding in the open form. To solve the Fe3+-loaded, domain-opened structure, an ovotransferrin N-lobe crystal that had been grown as the apo form was soaked with Fe3+-nitrilotriacetate, and its structure was solved at 2.1 A resolution. The Fe3+-soaked form showed almost exactly the same overall open structure as the iron-free apo form. The electron density map unequivocally proved the presence of an iron atom with the coordination by the two protein ligands of Tyr92-OH and Tyr191-OH. Other Fe3+ coordination sites are occupied by a nitrilotriacetate anion, which is stabilized through the hydrogen bonds with the peptide NH groups of Ser122, Ala123, and Gly124 and a side chain group of Thr117. There is, however, no clear interaction between the nitrilotriacetate anion and the synergistic anion binding site, Arg121.

  • Organizational Affiliation

    Research Institute for Food Science, Kyoto University, Uji, Kyoto 6110011, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (OVOTRANSFERRIN)329Gallus gallusMutation(s): 0 
Find proteins for P02789 (Gallus gallus)
Explore P02789 
Go to UniProtKB:  P02789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02789
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.29α = 90
b = 125.29β = 90
c = 87.53γ = 120
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations