4WCH

Structure of Isolated D Chain of Gigant Hemoglobin from Glossoscolex paulistus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the giant haemoglobin from Glossoscolex paulistus.

Ruggiero Bachega, J.F.Vasconcelos Maluf, F.Andi, B.D'Muniz Pereira, H.Falsarella Carazzollea, M.Orville, A.M.Tabak, M.Brandao-Neto, J.Garratt, R.C.Horjales Reboredo, E.

(2015) Acta Crystallogr.,Sect.D 71: 1257-1271

  • DOI: 10.1107/S1399004715005453
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The sequences of all seven polypeptide chains from the giant haemoglobin of the free-living earthworm Glossoscolex paulistus (HbGp) are reported together with the three-dimensional structure of the 3.6 MDa complex which they form. The refinement of t ...

    The sequences of all seven polypeptide chains from the giant haemoglobin of the free-living earthworm Glossoscolex paulistus (HbGp) are reported together with the three-dimensional structure of the 3.6 MDa complex which they form. The refinement of the full particle, which has been solved at 3.2 Å resolution, the highest resolution reported to date for a hexagonal bilayer haemoglobin composed of 12 protomers, is reported. This has allowed a more detailed description of the contacts between subunits which are essential for particle stability. Interpretation of features in the electron-density maps suggests the presence of metal-binding sites (probably Zn(2+) and Ca(2+)) and glycosylation sites, some of which have not been reported previously. The former appear to be important for the integrity of the particle. The crystal structure of the isolated d chain (d-HbGp) at 2.1 Å resolution shows different interchain contacts between d monomers compared with those observed in the full particle. Instead of forming trimers, as seen in the complex, the isolated d chains associate to form dimers across a crystallographic twofold axis. These observations eliminate the possibility that trimers form spontaneously in solution as intermediates during the formation of the dodecameric globin cap and contribute to understanding of the possible ways in which the particle self-assembles.


    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isolated Chain D of Gigant Hemoglobin from Glossoscolex Paulistus
D
140Glossoscolex paulistusMutation(s): 0 
Find proteins for A0A0M3KKZ2 (Glossoscolex paulistus)
Go to UniProtKB:  A0A0M3KKZ2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
D
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: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 53.110α = 90.00
b = 63.150β = 90.00
c = 78.386γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
GDAdata collection
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-24
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Advisory, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy