3AT5

Side-necked turtle (Pleurodira, Chelonia, REPTILIA) hemoglobin: cDNA-derived primary structures and X-ray crystal structures of Hb A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


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Literature

Side-necked turtle (Pleurodira, Chelonia, reptilia) hemoglobin: cDNA-derived primary structures and X-ray crystal structures of Hb A.

Hasegawa, T.Shishikura, F.Kuwada, T.

(2011) Iubmb Life 63: 188-196

  • DOI: 10.1002/iub.429
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Red blood cells of yellow-spotted river turtles (Podocnemis unifilis, Pleurodira, Chelonia, REPTILIA) have two hemoglobin (Hb) components, Hb A and Hb D. We purified the hemoglobin component homologous to amniote (reptiles, birds, and mammals) adult ...

    Red blood cells of yellow-spotted river turtles (Podocnemis unifilis, Pleurodira, Chelonia, REPTILIA) have two hemoglobin (Hb) components, Hb A and Hb D. We purified the hemoglobin component homologous to amniote (reptiles, birds, and mammals) adult Hb A which comprises two identical α(A) -globin polypeptides and two identical β-globin polypeptides. To establish the crystal structure of Podocnemis Hb A, we first determined the globin primary structures using cDNA nucleotide sequencing with the assistance of protein sequencing. The purified Podocnemis Hb A produced a different form of crystal for each of the two different buffer systems used: form A, tetragonal crystals (space group, P4₁2₁2), produced under neutral pH (pH 7-8) conditions; and form B, hexagonal crystals (space group, P6₁22), produced under high alkaline pH (pH 11-13) conditions. Single crystals of the two forms were examined by Raman microscopy with an excitation of 532 nm, indicating their structural differences. The crystal structures of the two forms were constructed by X-ray crystallographic diffraction at a resolution of 2.20 Å for form A and 2.35 Å for form B. The differences of the tertiary and quaternary structures of the two forms were marginal; however, one clear difference was found in helix structure. When comparing Podocnemis Hb A with Hb A from specimens in other taxa, such as Anser indicus (birds) and Homo sapiens (mammals) by SHELXPRO, the root mean square deviation (RMSD) between the corresponding Cα atoms of the two globins does not exceed 2.0 Å. These low values indicate the crystal structures resemble each other. Our data on X-ray crystal structures and Raman spectra not only reveal the first findings on the two crystal forms of Podocnemis unifilis Hb A but also provide the first refined models for reptilian adult Hb A.


    Organizational Affiliation

    Rigaku Corporation, Matsubara-cho, Akishima-shi, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlphaA-globin
A
141Podocnemis unifilisMutation(s): 0 
Gene Names: HBAA
Find proteins for E5RWQ0 (Podocnemis unifilis)
Go to UniProtKB:  E5RWQ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-globin
B
146Podocnemis unifilisMutation(s): 0 
Gene Names: HBB
Find proteins for E5RWQ1 (Podocnemis unifilis)
Go to Gene View: HBB
Go to UniProtKB:  E5RWQ1
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: 2.2 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.935α = 90.00
b = 85.935β = 90.00
c = 103.779γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata collection
CNXphasing
CNXrefinement
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance