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 
  • R-Value Observed: 0.210 

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This is version 1.3 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 D Biol Crystallogr 71: 1257-1271

  • DOI: https://doi.org/10.1107/S1399004715005453
  • Primary Citation of Related Structures:  
    4U8U, 4WCH

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isolated Chain D of Gigant Hemoglobin from Glossoscolex PaulistusA [auth D]140Glossoscolex paulistusMutation(s): 0 
UniProt
Find proteins for A0A0M3KKZ2 (Glossoscolex paulistus)
Explore A0A0M3KKZ2 
Go to UniProtKB:  A0A0M3KKZ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKZ2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
OXY
Query on OXY

Download Ideal Coordinates CCD File 
C [auth D]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.11α = 90
b = 63.15β = 90
c = 78.386γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
GDAdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Advisory, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Refinement description