2D2N: Structure Of An Extracellular Giant Hemoglobin Of The Gutless Beard Worm Oligobrachia Mashikoi

Mouthless and gutless marine animals, pogonophorans and vestimentiferans, obtain their nutrition solely from their symbiotic chemoautotrophic sulfur-oxidizing bacteria. These animals have sulfide-binding 400-kDa and/or 3,500-kDa Hb, which transports oxygen and sulfide simultaneously. The symbiotic bacteria are supplied with sulfide by Hb of the host animal and use it to provide carbon compounds. Here, we report the crystal structure of a 400-kDa Hb from pogonophoran Oligobrachia mashikoi at 2.85-A resolution. The structure is hollow-spherical, composed of a total of 24 globins as a dimer of dodecamer. This dodecameric assemblage would be a fundamental structural unit of both 400-kDa and 3,500-kDa Hbs. The structure of the mercury derivative used for phasing provides insights into the sulfide-binding mechanism. The mercury compounds bound to all free Cys residues that have been expected as sulfide-binding sites. Some of the free Cys residues are surrounded by Phe aromatic rings, and mercury atoms come into contact with these residues in the derivative structure. It is strongly suggested that sulfur atoms bound to these sites could be stabilized by aromatic-electrostatic interactions by the surrounding Phe residues.
PDB ID: 2D2NDownload
MMDB ID: 35818
PDB Deposition Date: 2005/9/12
Updated in MMDB: 2005/11
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Similar Structures:
Biological Unit for 2D2N: 24-meric; determined by author
Molecular Components in 2D2N
Label Count Molecule
Proteins (24 molecules)
Giant Hemoglobin, A1(b) Globin Chain
Molecule annotation
Giant Hemoglobin, A2(a5) Globin Chain
Molecule annotation
Giant Hemoglobin, B2(c) Globin Chain
Molecule annotation
Giant Hemoglobin, B1(d) Globin Chain
Molecule annotation
Chemicals (72 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB