Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

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

Macromolecule Content

• Total Structure Weight: 66139.23 
• Atom Count: 4656 
• Residue Count: 578 
• Unique protein chains: 2

1HBH

STRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII AND STRUCTURAL BASIS OF THE ROOT EFFECT

• DOI: 10.2210/pdb1HBH/pdb

• Classification: OXYGEN CARRIER
• Organism(s): Pseudotrematomus bernacchii


• Deposited: 1995-02-22 Released: 1995-04-20 
• Deposition Author(s): Ito, N., Komiyama, N.H., Fermi, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.220 
• R-Value Work: 0.160 

Literature

Structure of deoxyhaemoglobin of the antarctic fish Pagothenia bernacchii with an analysis of the structural basis of the root effect by comparison of the liganded and unliganded haemoglobin structures.

Ito, N., Komiyama, N.H., Fermi, G.

(1995) J.Mol.Biol. 250: 648-658

• PubMed: 7623382 
• DOI: 10.1006/jmbi.1995.0405


• PubMed Abstract: 
  

We have determined the structure of deoxyhaemoglobin from the antarctic fish Pagothenia bernacchii at pH 6.2 to a resolution of 2.2 A with X-ray data from a twinned crystal deconvoluted so as to approximate data from a single crystal. The R-factor between the (twinned) model and the observed data is 16% for reflections used in refinement and 22% for reflections not used in refinement. The T (deoxy) structure was compared with the R (liganded) structure at pH 8.0 in an attempt to understand the structural basis of the greater affinity for hydrogen ions of T, relative to R, that comprises the Root effect. Up to half of the effect can be attributed to interaction of the residues Asp95 (G1)alpha and Asp101 (G3)beta: in R the residues are far apart and their carboxyl groups are unprotonated, but the shift at the alpha 1 beta 2 interface that accompanies the R to T transition brings them so close that they appear to share a proton between them. The proximity of Asp99 (G1)beta may contribute to the required raising of the pKa values of the other two Asp residues. These and neighbouring residues are sufficiently conserved in the haemoglobins of trout (component IV), carp and bluefin tuna, all of which exhibit the Root effect, for the same mechanism to apply. However, the environment is equally conserved in haemoglobins of Trematomus newnesi (major component) and trout (component I), which do not exhibit the Root effect, so that the structural factors controlling the Asp-Asp interaction remain unclear. No other residue appears to undergo an R to T change in the immediate neighbourhoods that could account for any significant portion of the Root effect, so at least half of the effect must result either from long-range electrostatic interactions or from a large number of local interactions.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN (DEOXY) (ALPHA CHAIN)	A, C	143	Pseudotrematomus bernacchii	Mutation(s): 0  Gene Names: hba
Find proteins for P80043 (Pseudotrematomus bernacchii) Go to UniProtKB:  P80043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
HEMOGLOBIN (DEOXY) (BETA CHAIN)	B, D	146	Pseudotrematomus bernacchii	Mutation(s): 0  Gene Names: hbb
Find proteins for P80044 (Pseudotrematomus bernacchii) Go to UniProtKB:  P80044

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
HEM	A, B, C, D	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ACE	A, C	NON-POLYMER	C2 H4 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.220 
• R-Value Work: 0.160 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 62.650	α = 90.00
b = 96.300	β = 90.00
c = 62.650	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-02-22 
• Released Date: 1995-04-20 
• Deposition Author(s): Ito, N., Komiyama, N.H., Fermi, G.

Revision History 

• Version 1.0: 1995-04-20
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance