3VRG

The crystal structure of hemoglobin from woolly mammoth in the met form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of haemoglobin from woolly mammoth in liganded and unliganded states.

Noguchi, H.Campbell, K.L.Ho, C.Unzai, S.Park, S.-Y.Tame, J.R.H.

(2012) Acta Crystallogr.,Sect.D 68: 1441-1449

  • DOI: 10.1107/S0907444912029459
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The haemoglobin (Hb) of the extinct woolly mammoth has been recreated using recombinant genes expressed in Escherichia coli. The globin gene sequences were previously determined using DNA recovered from frozen cadavers. Although highly similar to the ...

    The haemoglobin (Hb) of the extinct woolly mammoth has been recreated using recombinant genes expressed in Escherichia coli. The globin gene sequences were previously determined using DNA recovered from frozen cadavers. Although highly similar to the Hb of existing elephants, the woolly mammoth protein shows rather different responses to chloride ions and temperature. In particular, the heat of oxygenation is found to be much lower in mammoth Hb, which appears to be an adaptation to the harsh high-latitude climates of the Pleistocene Ice Ages and has been linked to heightened sensitivity of the mammoth protein to protons, chloride ions and organic phosphates relative to that of Asian elephants. To elucidate the structural basis for the altered homotropic and heterotropic effects, the crystal structures of mammoth Hb have been determined in the deoxy, carbonmonoxy and aquo-met forms. These models, which are the first structures of Hb from an extinct species, show many features reminiscent of human Hb, but underline how the delicate control of oxygen affinity relies on much more than simple overall quaternary-structure changes.


    Organizational Affiliation

    Protein Design Laboratory, Yokohama City University, Suehiro 1-7-29, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit alpha
A
141Mammuthus primigeniusMutation(s): 0 
Gene Names: HBA-T2
Find proteins for D3U1H8 (Mammuthus primigenius)
Go to UniProtKB:  D3U1H8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hemoglobin subunit beta/delta hybrid
B
146Mammuthus primigeniusMutation(s): 0 
Gene Names: D (HBB)
Find proteins for D3U1H9 (Mammuthus primigenius)
Go to UniProtKB:  D3U1H9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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: 1.5 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.398α = 90.00
b = 61.473β = 110.08
c = 53.488γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release