7E99

Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 13% oxygen saturation

Summary for 7E99

• Entry DOI: 10.2210/pdb7e99/pdb
• Descriptor: Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B2, ... (7 entities in total)
• Functional Keywords: allostery, structural change, microspectrometry, crystal processing., oxygen transport
• Biological source: Oligobrachia mashikoi (Beard worm); More
• Total number of polymer chains: 4
• Total formula weight: 63424.55

Authors

Numoto, N.,Kawano, Y.,Okumura, H.,Baba, S.,Fukumori, Y.,Miki, K.,Ito, N. (deposition date: 2021-03-03, release date: 2021-10-06, Last modification date: 2024-10-09)

Primary citation

Numoto, N.,Kawano, Y.,Okumura, H.,Baba, S.,Fukumori, Y.,Miki, K.,Ito, N.
Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Iucrj, 8:954-962, 2021

PubMed Abstract: Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.

PubMed: 34804547
DOI: 10.1107/S2052252521009386

Experimental method

X-RAY DIFFRACTION (2.1 Å)