1NS9

The 1.6A Structure of Horse Methemoglobin at pH 7.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A pH-Dependent Aquomet-to-Hemichrome Transition in Crystalline Horse Methemoglobin

Robinson, V.L.Smith, B.B.Arnone, A.

(2003) Biochemistry 42: 10113-10125

  • DOI: 10.1021/bi030059t
  • Primary Citation of Related Structures:  1NS6

  • PubMed Abstract: 
  • In 1947, Perutz and co-workers reported that crystalline horse methemoglobin undergoes a large lattice transition as the pH is decreased from 7.1 to 5.4. We have determined the pH 7.1 and 5.4 crystal structures of horse methemoglobin at 1.6 and 2.1 A ...

    In 1947, Perutz and co-workers reported that crystalline horse methemoglobin undergoes a large lattice transition as the pH is decreased from 7.1 to 5.4. We have determined the pH 7.1 and 5.4 crystal structures of horse methemoglobin at 1.6 and 2.1 A resolution, respectively, and find that this lattice transition involves a 23 A translation of adjacent hemoglobin tetramers as well as changes in alpha heme ligation and the tertiary structure of the alpha subunits. Specifically, when the pH is lowered from 7.1 to 5.4, the Fe(3+) alpha heme groups (but not the beta heme groups) are converted from the aquomet form, in which the proximal histidine [His87(F8)alpha] and a water molecule are the axial heme ligands, to the hemichrome (bishistidine) form, in which the proximal histidine and the distal histidine [His58(E7)alpha] are the axial heme ligands. Hemichrome formation is coupled to a large tertiary structure transition in the eight-residue segment Pro44(CD2)alpha-Gly51(D7)alpha that converts from an extended loop structure at pH 7.1 to a pi-like helix at pH 5.4. The formation of the pi helix forces Phe46(CD4)alpha out of the alpha heme pocket and into the interface between adjacent hemoglobin tetramers where it participates in crystal lattice contacts unique to the pH 5.4 structure. In addition, the transition from aquomet alpha subunits to bishistidine alpha subunits is accompanied by an approximately 1.2 A movement of the alpha heme groups to a more solvent-exposed position as well as the creation of a solvent channel from the interior of the alpha heme pocket to the outside of the tetramer. These changes and the extensive rearrangement of the crystal lattice structure allow the alpha heme group of one tetramer to make direct contact with an alpha heme group on an adjacent tetramer. These results suggest possible functional roles for hemichrome formation in vivo.


    Related Citations: 
    • The Structure of Haemoglobin. III. Direct Determination of the Molecular Transform
      Perutz, M.F.
      (1954) Proc.R.Soc.London,Ser.B 225: 264
    • An X-Ray Study of Horse Methaemoglobin. I
      Boyes-Watson, J.,Davidson, E.,Perutz, M.F.
      (1947) Proc.R.Soc.London,Ser.B 191: 83


    Organizational Affiliation

    Department of Biochemistry, College of Medicine, The University of Iowa, Iowa City, Iowa 52242, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin alpha subunit
A
141Equus caballusGene Names: HBA
Find proteins for P01958 (Equus caballus)
Go to UniProtKB:  P01958
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin beta subunit
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: 1.6 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.400α = 90.00
b = 63.200β = 110.90
c = 54.600γ = 90.00
Software Package:
Software NamePurpose
SDMSdata scaling
SDMSdata reduction
REFMACrefinement
CNSrefinement
SDMSdata collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance