1V4U

Crystal structure of bluefin tuna carbonmonoxy-hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A STRUCTURAL EXPLANATION OF THE ROOT EFFECT

Yokoyama, T.Chong, K.T.Miyazaki, G.Morimoto, H.Shih, D.T.Unzai, S.Tame, J.R.Park, S.Y.

(2004) J.Biol.Chem. 279: 28632-28640

  • DOI: 10.1074/jbc.M401740200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structure of hemoglobin has been known for several decades, yet various features of the molecule remain unexplained or controversial. Several animal hemoglobins have properties that cannot be readily explained in terms of their amino acid ...

    The crystal structure of hemoglobin has been known for several decades, yet various features of the molecule remain unexplained or controversial. Several animal hemoglobins have properties that cannot be readily explained in terms of their amino acid sequence and known atomic models of hemoglobin. Among these, fish hemoglobins are well known for their widely varying interactions with heterotropic effector molecules and pH sensitivity. Some fish hemoglobins are almost completely insensitive to pH (within physiological limits), whereas others show extremely low oxygen affinity under acid conditions, a phenomenon called the Root effect. X-ray crystal structures of Root effect hemoglobins have not, to date, provided convincing explanations of this effect. Sequence alignments have signally failed to pinpoint the residues involved, and site-directed mutagenesis has not yielded a human hemoglobin variant with this property. We have solved the crystal structure of tuna hemoglobin in the deoxy form at low and moderate pH and in the presence of carbon monoxide at high pH. A comparison of these models shows clear evidence for novel mechanisms of pH-dependent control of ligand affinity.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Suehiro-cho 1-7-29, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hemoglobin alpha chain
A, C
144Thunnus thynnusMutation(s): 0 
Find proteins for Q8AYM0 (Thunnus thynnus)
Go to UniProtKB:  Q8AYM0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
hemoglobin beta chain
B, D
146Thunnus thynnusMutation(s): 0 
Find proteins for Q8AYM1 (Thunnus thynnus)
Go to UniProtKB:  Q8AYM1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.016α = 90.00
b = 102.541β = 90.00
c = 108.451γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-06
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance