Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.13 kDa 
• Atom Count: 2636 
• Residue Count: 289 
• Unique protein chains: 2

3GKV

X-ray structure of an intermediate along the oxidation pathway of Trematomus bernacchii hemoglobin

• DOI: 10.2210/pdb3GKV/pdb

• Classification: OXYGEN TRANSPORT
• Organism(s): Trematomus bernacchii
• Mutation(s): Yes 


• Deposited: 2009-03-11 Released: 2009-05-05 
• Deposition Author(s): Merlino, A., Vitagliano, L., Sica, F., Vergara, A., Mazzarella, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Combined crystallographic and spectroscopic analysis of Trematomus bernacchii hemoglobin highlights analogies and differences in the peculiar oxidation pathway of Antarctic fish hemoglobins

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

(2009) Biopolymers 91: 1117-1125

• PubMed: 19373928 
• DOI: 10.1002/bip.21206
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Recent studies have demonstrated that hemoglobins isolated from Antarctic fish undergo peculiar oxidation processes. Here we show, by combining crystallographic and spectroscopic data, that the oxidation pathway of Trematomus bernacchii hemoglobin (HbTb) is distinct from that observed for the major component of Trematomus newnesi (Hb1Tn), despite the high sequence identity of the two proteins and structural similarity of their ferrous and fully oxidized states. Resonance Raman analysis of HbTb autoxidation upon air-exposure reveals the absence of the oxidized pentacoordinated state that was observed for Hb1Tn. The HbTb oxidation pathway is characterized by two ferric species: an aquo hexacoordinated high spin state and a bis-histidyl hexacoordinated low spin form, which appear in the early stages of the oxidation process. The high resolution structure of an intermediate along the oxidation pathway has been determined at 1.4 A resolution. The analysis of the electron density of the heme pocket shows, for both the alpha and the beta iron, the coexistence of multiple binding states. In this partially oxidized form, HbTb exhibits significant deviations from the canonical R state both at the local and global level. The analysis of these modifications highlights the structural correlation between key functional regions of the protein.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Chemistry, University of Naples, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin subunit alpha	A	143	Trematomus bernacchii	Mutation(s): 1  Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii) Explore P80043  Go to UniProtKB:  P80043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin subunit beta	B	146	Trematomus bernacchii	Mutation(s): 0  Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii) Explore P80044  Go to UniProtKB:  P80044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CMO	A, B	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.211 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.88	α = 90
b = 87.647	β = 100.17
c = 55.339	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-11 
• Released Date: 2009-05-05 
Deposition Author(s): Merlino, A., Vitagliano, L., Sica, F., Vergara, A., Mazzarella, L.

Revision History 

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance