3D1K

R/T intermediate quaternary structure of an antarctic fish hemoglobin in an alpha(CO)-beta(pentacoordinate) state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

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


Literature

Spectroscopic and crystallographic characterization of a tetrameric hemoglobin oxidation reveals structural features of the functional intermediate relaxed/tense state.

Vitagliano, L.Vergara, A.Bonomi, G.Merlino, A.Verde, C.di Prisco, G.Howes, B.D.Smulevich, G.Mazzarella, L.

(2008) J Am Chem Soc 130: 10527-10535

  • DOI: https://doi.org/10.1021/ja803363p
  • Primary Citation of Related Structures:  
    3D1K

  • PubMed Abstract: 

    Tetrameric hemoglobins represent the most commonly used model for the description of the basic concepts of protein allostery. The classical stereochemical model assumes a concerted transition of the protein, upon oxygen release, from the relaxed (R) to the tense (T) state. Despite the large amount of data accumulated on the end-points of the transition, scarce structural information is available on the intermediate species along the pathway. Here we report a spectroscopic characterization of the autoxidation process of the Trematomus newnesi major Hb component and the atomic resolution structure (1.25 A) of an intermediate form along the pathway characterized by a different binding and oxidation state of the alpha and beta chains. In contrast to the alpha-heme iron, which binds a CO molecule, the beta iron displays a pentacoordinated oxidized state, which is rare in tetrameric hemoglobins. Interestingly, the information provided by the present analysis is not limited to the characterization of the peculiar oxidation process of Antarctic fish hemoglobins. Indeed, this structure represents the most detailed snapshot of hemoglobin allosteric transition hitherto achieved. Upon ligand release at the beta heme, a cascade of structural events is observed. Notably, several structural features of the tertiary structure of the alpha and beta chains closely resemble those typically observed in the deoxygenated state. The overall quaternary structure also becomes intermediate between the R and the T state. The analysis of the alterations induced by the ligand release provides a clear picture of the temporal sequence of the events associated with the transition. The implications of the present findings have also been discussed in the wider context of tetrameric Hbs.


  • Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha-1142Trematomus newnesiMutation(s): 0 
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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta-1/2146Trematomus 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: 1.25 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.458α = 90
b = 87.664β = 99.16
c = 55.502γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data 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: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description