3SDH

HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution crystallographic analysis of a co-operative dimeric hemoglobin.

Royer Jr., W.E.

(1994) J.Mol.Biol. 235: 657-681

  • DOI: 10.1006/jmbi.1994.1019
  • Primary Citation of Related Structures:  4SDH

  • PubMed Abstract: 
  • High-resolution crystal structures of the co-operative dimeric hemoglobin from the blood clam Scapharca inaequivalvis have been determined in the unliganded (deoxy) and carbon monoxide (CO) liganded states. The deoxy structure has been refined at 1.6 ...

    High-resolution crystal structures of the co-operative dimeric hemoglobin from the blood clam Scapharca inaequivalvis have been determined in the unliganded (deoxy) and carbon monoxide (CO) liganded states. The deoxy structure has been refined at 1.6 A resolution to an R-factor of 0.158 and the CO structure has been refined at 1.4 A resolution to an R-factor of 0.159. These structures reveal details of the structural transitions involved in co-operative ligand binding that involve only a minor rotation of subunits but very striking tertiary changes at the interface. A small number of residues in the F-helix appear to mediate co-operativity in this simple hemoglobin. The oxygen affinity of each subunit appears to be largely dictated by the disposition of phenylalanine 97, whose side-chain packs in the heme pocket in the deoxy state but is extruded towards the interface in the CO-liganded structure. Direct involvement of the ligand-binding heme group is a novel feature of the subunit interface and appears important for intersubunit communication. Ligation alters the conformation of the heme propionate groups along with two interacting residues from the symmetry-related subunit. These two residues, lysine 96 and asparagine 100, link the heme of one subunit with the F-helix of the second subunit in such a way as to influence the ligand affinity of that subunit. The interface is highly hydrated by well-ordered water molecules that are likely to be important in the stabilization of the two structures.


    Related Citations: 
    • Structural Transitions Upon Ligand Binding in a Cooperative Dimeric Hemoglobin
      Royer Junior, W.E.,Hendrickson, W.A.,Chiancone, E.
      (1990) Science 249: 518
    • The 2.4 Angstroms Crystal Structure of Scapharca Dimeric Hemoglobin. Cooperatively Based on Directly Communicating Hemes at a Novel Subunit Interface
      Royer Junior, W.E.,Hendrickson, W.A.,Chiancone, E.
      (1989) J.Biol.Chem. 264: 21052


    Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical Center, Worcester 01605.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEMOGLOBIN I (CARBONMONOXY)
A, B
146Anadara inaequivalvisN/A
Find proteins for P02213 (Anadara inaequivalvis)
Go to UniProtKB:  P02213
Small Molecules
Ligands 2 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
CMO
Query on CMO

Download SDF File 
Download CCD File 
A, B
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 93.250α = 90.00
b = 43.980β = 122.03
c = 83.500γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1993-06-23 
  • Released Date: 1993-10-31 
  • Deposition Author(s): Royerjunior, W.E.
  • This entry supersedes: 1SDH

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance