1TFA | pdb_00001tfa

OVOTRANSFERRIN, N-TERMINAL LOBE, APO FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.243 (Depositor) 
  • R-Value Work: 
    0.187 (Depositor) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

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 Biological Chem 274: 10190-10194

  • DOI: https://doi.org/10.1074/jbc.274.15.10190
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 36.63 kDa 
  • Atom Count: 2,844 
  • Modeled Residue Count: 329 
  • Deposited Residue Count: 329 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN (OVOTRANSFERRIN)329Gallus gallusMutation(s): 0 
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.243 (Depositor) 
  • R-Value Work:  0.187 (Depositor) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.17α = 90
b = 125.17β = 90
c = 87.26γ = 120
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
PHASESphasing
X-PLORrefinement

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: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary