Biological Assembly 1  

 3D View: Structure | 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.

Macromolecule Content

• Total Structure Weight: 33210.69 
• Atom Count: 2242 
• Residue Count: 289 
• Unique protein chains: 2

1LA6

The crystal structure of Trematomus newnesi hemoglobin in a partial hemichrome state

• DOI: 10.2210/pdb1LA6/pdb

• Classification: OXYGEN STORAGE/TRANSPORT
• Organism(s): Trematomus newnesi


• Deposited: 2002-03-28 Released: 2002-07-31 
• Deposition Author(s): Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A., Mazzarella, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.212 
• R-Value Work: 0.179 

Literature

The crystal structure of a tetrameric hemoglobin in a partial hemichrome state

Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A., Mazzarella, L.

(2002) Proc.Natl.Acad.Sci.USA 99: 9801-9806

• PubMed: 12093902 
• DOI: 10.1073/pnas.132182099
• Also Cited By: 1S5Y, 1S5X


• PubMed Abstract: 
  

Tetrameric hemoglobins are the most widely used systems in studying protein cooperativity. Allosteric effects in hemoglobins arise from the switch between a relaxed (R) state and a tense (T) state occurring upon oxygen release. Here we report the 2.0-A crystal structure of the main hemoglobin component of the Antarctic fish Trematomus newnesi, in a partial hemichrome form. The two alpha-subunit iron atoms are bound to a CO molecule, whereas in the beta subunits the distal histidine residue is the sixth ligand of the heme iron. This structure, a tetrameric hemoglobin in the hemichrome state, demonstrates that the iron coordination by the distal histidine, usually associated with denaturing states, may be tolerated in a native-like hemoglobin structure. In addition, several features of the tertiary and quaternary organization of this structure are intermediate between the R and T states and agree well with the R --> T transition state properties obtained by spectroscopic and kinetic techniques. The analysis of this structure provides a detailed pathway of heme-heme communication and it indicates that the plasticity of the beta heme pocket plays a role in the R --> T transition of tetrameric hemoglobins.

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Related Citations: 

• Liganded and unliganded forms of Antarctic fish haemoglobins in polyethylene glycol: crystallization of an R-state haemichrome intermediate
  Riccio, A.,Vitagliano, L.,di Prisco, G.,Zagari, A.,Mazzarella, L.
  (2001) Acta Crystallogr. 57: 1144
• Crystal structure of Trematomus newnesi haemoglobin re-opens the root effect question
  Mazzarella, L.,D'Avino, R.,di PRISCO, G.,Savino, C.,VITAGLIANO, L.,MOODY, P.C.E.,ZAGARI, A.
  (1999) J.Mol.Biol. 287: 897




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Organizational Affiliation: 

Istituto di Biochimica delle Proteine ed Enzimologia, Consiglio Nazionale delle Ricerche, I-80125 Naples, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin alpha-1 chain	A	143	Trematomus newnesi	Gene Names: hba1
Find proteins for P45718 (Trematomus newnesi) Go to UniProtKB:  P45718

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Hemoglobin beta-1/2 chain	B	146	Trematomus newnesi
Find proteins for P45720 (Trematomus newnesi) Go to UniProtKB:  P45720

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.212 
• R-Value Work: 0.179 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 89.853	α = 90.00
b = 88.190	β = 97.79
c = 55.142	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-28 
• Released Date: 2002-07-31 
• Deposition Author(s): Riccio, A., Vitagliano, L., di Prisco, G., Zagari, A., Mazzarella, L.

Revision History 

• Version 1.0: 2002-07-31
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance