6RP5

Crystal structure of monocarboxylated hemoglobin from the sub-Antarctic fish Eleginops maclovinus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The unique structural features of carbonmonoxy hemoglobin from the sub-Antarctic fish Eleginops maclovinus.

Balasco, N.Vitagliano, L.Merlino, A.Verde, C.Mazzarella, L.Vergara, A.

(2019) Sci Rep 9: 18987-18987

  • DOI: 10.1038/s41598-019-55331-3

  • PubMed Abstract: 
  • Tetrameric hemoglobins (Hbs) are prototypical systems for the investigations of fundamental properties of proteins. Although the structure of these proteins has been known for nearly sixty years, there are many aspects related to their function/struc ...

    Tetrameric hemoglobins (Hbs) are prototypical systems for the investigations of fundamental properties of proteins. Although the structure of these proteins has been known for nearly sixty years, there are many aspects related to their function/structure that are still obscure. Here, we report the crystal structure of a carbonmonoxy form of the Hb isolated from the sub-Antarctic notothenioid fish Eleginops maclovinus characterised by either rare or unique features. In particular, the distal site of the α chain results to be very unusual since the distal His is displaced from its canonical position. This displacement is coupled with a shortening of the highly conserved E helix and the formation of novel interactions at tertiary structure level. Interestingly, the quaternary structure is closer to the T-deoxy state of Hbs than to the R-state despite the full coordination of all chains. Notably, these peculiar structural features provide a rationale for some spectroscopic properties exhibited by the protein in solution. Finally, this unexpected structural plasticity of the heme distal side has been associated with specific sequence signatures of various Hbs.


    Organizational Affiliation

    Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, 80131, Naples, Italy.,Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy.,Dept. Chemical Sciences, University of Napoli "Federico II", Via Cinthia, 80126, Naples, Italy. avergara@unina.it.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Naples, Italy. luigi.vitagliano@unina.it.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha 1
A
143Eleginops maclovinusMutation(s): 0 
Gene Names: hba1
Find proteins for K7N5M5 (Eleginops maclovinus)
Go to UniProtKB:  K7N5M5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta-1
B
144Eleginops maclovinusMutation(s): 0 
Gene Names: hbb1
Find proteins for K7N5M6 (Eleginops maclovinus)
Go to UniProtKB:  K7N5M6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DTN
Query on DTN

Download SDF File 
Download CCD File 
A
DITHIONITE
O4 S2
GRWZHXKQBITJKP-UHFFFAOYSA-L
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.168 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.702α = 90.00
b = 91.702β = 90.00
c = 168.716γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release