1IBE | pdb_00001ibe

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.230 (Depositor) 
  • R-Value Work: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1IBE

This is version 1.4 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 Biology 264: 743-756

  • DOI: https://doi.org/10.1006/jmbi.1996.0674
  • Primary Citation Related Structures: 
    1IBE

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 32.39 kDa 
  • Atom Count: 2,484 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 287 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEMOGLOBIN (DEOXY)141Equus caballusMutation(s): 1 
UniProt
Find proteins for P01958 (Equus caballus)
Explore P01958 
Go to UniProtKB:  P01958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01958
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
HEMOGLOBIN (DEOXY)146Equus caballusMutation(s): 0 
UniProt
Find proteins for P02062 (Equus caballus)
Explore P02062 
Go to UniProtKB:  P02062
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02062
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.230 (Depositor) 
  • R-Value Work:  0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.18α = 90
b = 63.18β = 111.1
c = 54.58γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement
UCSDdata reduction
UCSDdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-21
    Changes: Data collection, Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations