Crystal structure of CO-HbI transformed to an unligated state

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

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Ligand-linked structural transitions in crystals of a cooperative dimeric hemoglobin.

Knapp, J.E.Royer Jr., W.E.

(2003) Biochemistry 42: 4640-4647

  • DOI: https://doi.org/10.1021/bi027136p
  • Primary Citation of Related Structures:  
    1NWI, 1NWN, 1NXF

  • PubMed Abstract: 

    Cooperative ligand binding in the dimeric hemoglobin (HbI) from the blood clam Scapharca inaequivalvis is mediated primarily by tertiary structural changes, but with a small quaternary rearrangement (approximately 3 degrees), based on analysis of distinct crystal forms for ligated and unligated molecules. We report here ligand transition structures in both crystal forms. Binding CO to unligated HbI crystals results in a structure that approaches, but does not attain, the full allosteric transition. In contrast, removing CO from the HbI-CO crystals results in a structure that possesses all the key low affinity attributes previously identified from analysis of HbI crystals grown in the unligated state. Subsequent binding of CO shows the reversibility of this process. The observed structural changes include the quaternary rearrangement even under the constraints of lattice interactions, demonstrating that subunit rotation is an integral component of the ligand-linked structural transition in HbI. Analysis of both crystal forms, along with data from HbI mutants, suggests that the quaternary structural change is linked to the movement of the heme group, supporting a hypothesis that the heme movement is the central event that triggers cooperative ligand binding in this hemoglobin dimer. These results show both the effects of a crystal lattice in limiting quaternary structural transitions and provide the first example of complete allosteric transitions within another crystal lattice.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
globin I
A, B, C, D
146Anadara inaequivalvisMutation(s): 0 
Gene Names: HbI
Find proteins for P02213 (Anadara inaequivalvis)
Explore P02213 
Go to UniProtKB:  P02213
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02213
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.81α = 90
b = 44.21β = 115.38
c = 87.12γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description