4HRT

Scapharca tetrameric hemoglobin, unliganded


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tertiary and Quaternary Allostery in Tetrameric Hemoglobin from Scapharca inaequivalvis.

Ronda, L.Bettati, S.Henry, E.R.Kashav, T.Sanders, J.M.Royer, W.E.Mozzarelli, A.

(2013) Biochemistry 52: 2108-2117

  • DOI: 10.1021/bi301620x
  • Primary Citation of Related Structures:  4HRR

  • PubMed Abstract: 
  • The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied ...

    The clam Scapharca inaequivalvis possesses two cooperative oxygen binding hemoglobins in its red cells: a homodimeric HbI and a heterotetrameric A2B2 HbII. Each AB dimeric half of HbII is assembled in a manner very similar to that of the well-studied HbI. This study presents crystal structures of HbII along with oxygen binding data both in the crystalline state and in wet nanoporous silica gels. Despite very similar ligand-linked structural transitions observed in HbI and HbII crystals, HbII in the crystal or encapsulated in silica gels apparently exhibits minimal cooperativity in oxygen binding, in contrast with the full cooperativity exhibited by HbI crystals. However, oxygen binding curves in the crystal indicate the presence of a significant functional inequivalence of A and B chains. When this inequivalence is taken into account, both crystal and R state gel functional data are consistent with the conservation of a tertiary contribution to cooperative oxygen binding, quantitatively similar to that measured for HbI, and are in keeping with the structural information. Furthermore, our results indicate that to fully express cooperative ligand binding, HbII requires quaternary transitions hampered by crystal lattice and gel encapsulation, revealing greater complexity in cooperative function than the direct communication across a dimeric interface observed in HbI.


    Organizational Affiliation

    Department of Pharmacy, University of Parma , Parco Area delle Scienze, 23/A, 43124 Parma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Globin-2 A chain
A, C, E, G
150Anadara inaequivalvisN/A
Find proteins for P14821 (Anadara inaequivalvis)
Go to UniProtKB:  P14821
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin B chain
B, D, F, H
152Anadara inaequivalvisN/A
Find proteins for P14822 (Anadara inaequivalvis)
Go to UniProtKB:  P14822
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B, C, D, E, F, G, H
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.133 
  • Space Group: P 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 94.353α = 90.00
b = 100.958β = 90.00
c = 127.165γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
HKL-2000data scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-10-28 
  • Released Date: 2012-12-12 
  • Deposition Author(s): Royer, W.E.

Revision History 

  • Version 1.0: 2012-12-12
    Type: Initial release
  • Version 1.1: 2013-04-10
    Type: Database references
  • Version 1.2: 2014-01-08
    Type: Database references