1LA6

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • 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 ...

    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.


    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


    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
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha-1 chain
A
143Trematomus newnesiGene Names: hba1
Find proteins for P45718 (Trematomus newnesi)
Go to UniProtKB:  P45718
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta-1/2 chain
B
146Trematomus newnesi
Find proteins for P45720 (Trematomus newnesi)
Go to UniProtKB:  P45720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
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: 2 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.853α = 90.00
b = 88.190β = 97.79
c = 55.142γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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