3NFE

The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1074/jbc.M110.143537
  • Primary Citation of Related Structures:  

  • 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 Tr ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha-1
A, C
143Trematomus newnesiMutation(s): 0 
Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Go to UniProtKB:  P45718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta-1/2
B, D
146Trematomus newnesiMutation(s): 0 
Find proteins for P45720 (Trematomus newnesi)
Go to UniProtKB:  P45720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, C
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.185 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 62.022α = 90.00
b = 62.022β = 90.00
c = 187.926γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CrystalCleardata collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance