3NG6

The crystal structure of hemoglobin I from Trematomus newnesi in deoxygenated state obtained through an oxidation/reduction cycle in which potassium hexacyanoferrate and sodium dithionite were alternatively added


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

An order-disorder transition plays a role in switching off the root effect in fish hemoglobins.

Vergara, A.Vitagliano, L.Merlino, A.Sica, F.Marino, K.Verde, C.di Prisco, G.Mazzarella, L.

(2010) J Biol Chem 285: 32568-32575

  • DOI: https://doi.org/10.1074/jbc.M110.143537
  • Primary Citation of Related Structures:  
    3NFE, 3NG6

  • PubMed Abstract: 

    The Root effect is a widespread property among fish hemoglobins whose structural basis remains largely obscure. Here we report a crystallographic and spectroscopic characterization of the non-Root-effect hemoglobin isolated from the Antarctic fish Trematomus newnesi in the deoxygenated form. The crystal structure unveils that the T state of this hemoglobin is stabilized by a strong H-bond between the side chains of Asp95α and Asp101β at the α(1)β(2) and α(2)β(1) interfaces. This unexpected finding undermines the accepted paradigm that correlates the presence of this unusual H-bond with the occurrence of the Root effect. Surprisingly, the T state is characterized by an atypical flexibility of two α chains within the tetramer. Indeed, regions such as the CDα corner and the EFα pocket, which are normally well ordered in the T state of tetrameric hemoglobins, display high B-factors and non-continuous electron densities. This flexibility also leads to unusual distances between the heme iron and the proximal and distal His residues. These observations are in line with Raman micro-spectroscopy studies carried out both in solution and in the crystal state. The findings here presented suggest that in fish hemoglobins the Root effect may be switched off through a significant destabilization of the T state regardless of the presence of the inter-aspartic H-bond. Similar mechanisms may also operate for other non-Root effect hemoglobins. The implications of the flexibility of the CDα corner for the mechanism of the T-R transition in tetrameric hemoglobins are also discussed.


  • Organizational Affiliation

    Department of Chemistry, University of Naples Federico II, Naples I-80126, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha-1
A, C
143Trematomus newnesiMutation(s): 1 
UniProt
Find proteins for P45718 (Trematomus newnesi)
Explore P45718 
Go to UniProtKB:  P45718
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45718
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta-1/2
B, D
146Trematomus newnesiMutation(s): 0 
UniProt
Find proteins for P45720 (Trematomus newnesi)
Explore P45720 
Go to UniProtKB:  P45720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45720
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.882α = 90
b = 61.882β = 90
c = 187.014γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description