1IBE

DEOXY-HAEMOGLOBIN TRAPPED IN THE HIGH-AFFINITY (R) STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • 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 horse deoxyhaemoglobin trapped in the high-affinity (R) state.

Wilson, J.Phillips, K.Luisi, B.

(1996) J.Mol.Biol. 264: 743-756

  • DOI: 10.1006/jmbi.1996.0674

  • PubMed Abstract: 
  • Co-operative oxygen binding by the vertebrate haemoglobins arises from an equilibrium between a quaternary structure with low affinity (T), favoured in the absence of ligand, and a high affinity form (R) adopted by the fully ligated protein. While R ...

    Co-operative oxygen binding by the vertebrate haemoglobins arises from an equilibrium between a quaternary structure with low affinity (T), favoured in the absence of ligand, and a high affinity form (R) adopted by the fully ligated protein. While R state haemoglobin has an oxygen affinity close to that of isolated subunits, the affinity of the T state is roughly 300-fold lower. The mechanism by which the T state restrains ligand binding, and the pathway of the quaternary transition, have been largely revealed by detailed crystallographic analyses of a number of haemoglobin molecules in the equilibrium states, as well as intermediate forms of the T state including partially ligated species. The ligation intermediates of the R state, however, have not been as well characterized structurally. We report here the crystal structure of one such intermediate species, namely, horse deoxyhaemoglobin in the R state, at 1.8 A resolution. While ligand binding in the T state may result in unfavourable stereochemistry in and around the haem-ligand complex, the more plastic R structure appears to accommodate equally well both liganded and ligand-free haem. Loss of ligand at the R state haem results in movements of the haem and shifts of the FG corners, which form characteristic intersubunit contacts that distinguish the quaternary states. The shifts are comparable in magnitude to the corresponding movements associated with de-ligation in the T state, although they differ in direction. These and other differences illustrate how the structural changes in the haem pocket are communicated to the subunit interfaces and how the movements that can occur in the R state may be impeded in the T state.


    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (DEOXY)
A
141Equus caballusGene Names: HBA
Find proteins for P01958 (Equus caballus)
Go to UniProtKB:  P01958
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN (DEOXY)
B
146Equus caballusGene Names: HBB
Find proteins for P02062 (Equus caballus)
Go to Gene View: HBB
Go to UniProtKB:  P02062
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.180α = 90.00
b = 63.180β = 111.10
c = 54.580γ = 90.00
Software Package:
Software NamePurpose
UCSDdata scaling
UCSDdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance