4. Problem to solve: Haemoglobin

The metalloprotein Haemoglobin (Hgb) is the iron-containing protein able to transport oxygen, essential to get energy from aerobic metabolic reactions, through red blood cells of almost every vertebrate. The first atomic structure of Hgb was determined in 1960 by X-ray crystallography [Perutz et al., 1960]. Hgb was, alongside myoglobin, the first structure solved by this methodology. Due to its emblematic prominence in structural biology History, we have selected Hgb to model its atomic structure.

Hgb is a relatively small macromolecule (molecular weight of 64 KDa) that shows C2 symmetry. This heterotetramer is constituted by four globular polypeptide subunits, two \alpha and two \beta monomers with 141 and 146 aminoacids in human Hgb, respectively. Each subunit associates to a prosthetic heme group, that consists in an iron (Fe) ion and the heterocyclic ring of porphyrin. Although the molecule is able of binding oxygen only in the reduced ferrous status, human Hgb is commercially distributed in its nonfunctional oxidized ferric status as metHgb. The atomic structure of the human metHgb specimen was inferred by Khoshouei et al. [2017] for the first time from the electron density volume obtained by cryo-EM and using the Volta phase plate. The volume, at 3.2Å resolution, and its atomic interpretation (Fig. 3.1) are available in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB) with accession numbers EMD-3488 and PDB-5NI1, respectively.

This tutorial will guide us in the deduction process of the human metHgb atomic structure using the Scipion framework, the 3D map and the protein sequences as starting input data, as well as reference atomic structures as homologous models in the way indicated in Martínez et al. [2020].