Examples and Instructions for Describing the Molecular System in an ADIT-NMR Deposition

Figure 1. Ligands, cofactors, and non-standard residues Chemical component Figure 2. Molecular entity Molecular entity Figure 3. Molecular assembly Molecular assembly


A BMRB deposition requires a description of the molecular system used to collect the reported data. The molecular system is described in a hierarchal manner starting with any non-standard residues and/or small molecules (chemical components) in the system. Next, the molecular entities that exist in the system and are in the sample (biopolymers and non-polymers, including metal ions, cofactors and other small molecules) are described. Finally, each instance of a molecular entity in the molecular system is given a name (i.e., polypeptide one and polypeptide two for a homodimer or strand one and strand two for a double stranded DNA system) and any unique characteristics provided. The three levels of the molecular system hierarchy are described in more detail below.

Ligands, cofactors, and non-standard residues (chemical components)

Ligands, cofactors, and non-standard residues are any non-polymer from a simple metal ion to a relatively complex molecule like a steriod, heme, or drug. These chemical components may represent either chemically complete molecules (Figure 1A) or chemical moieties like amino acid residues (Figure 1B) that are linked together to form more complex molecules. Ligands and cofactors must also be listed as 'Molecular entities' (Figure 2A, see below), but non-standard residues or other chemical components that are used to build more complex molecules are not described as molecular entities. In the ADIT-NMR section where ligands, cofactors, and non-standard residue are described, the name(s) for the molecule and a variety of molecular characteristics are entered. The individual atoms in the component are listed with their names and characteristics. Each chemical bond in the molecule is defined by the atoms involved in the bond and its type. If a description of a chemical component can be found in the PDB Ligand Depot or the BMRB ligand library, a depositor need only supply the name of the component and its ID and the remaining required information will be entered in the deposition processing stage by annotators.

Molecular entity (entity)

Molecular entities are chemically unique molecules that can be either a non-polymer (Figure 2A) or a polymer (Figure 2B). For polymers, the polymer type and residue sequence are required information. A molecular entity may represent either a single chemical component (Figure 2A) or two or more chemical components linked together as in a protein, nucleic acid polymer, or carbohydrate (Figure 2B).

Molecular assembly (assembly)

Molecular assemblies are composed of one or more molecular entities. A BMRB entry contains data obtained from one molecular assembly represented by the molecules (molecular entities) under study that are present in the sample tube. Many different types of molecular assemblies are possible, including small non-polymeric molecules (Figure 3A), single chain polymers (Figure 3B), homo or hetero multimeric biopolymer complexes possibly with ligands (Figure 3C), complexes in very slow to fast exchange with free ligands (Figure 3D). If the molecular assembly represents more than one molecule, the molecules may form either a tight or loose complex. A complete list of the molecules that make up the assembly is required. For molecular assembly shown in Figure 3C, the assembly molecule list contains four items even though two of the molecules (magenta) are chemically identical. The presence of any intra- or inter-molecular crosslinking bonds also needs to be reported.

Example molecular assemblies with instructions for entering a deposition

1) Ribonuclease (single chain polypeptide without ligands, Figure 3B):
2) Human zinc finger 2HX1 (single chain polypeptide with two zinc ligands):
3) Hemoglobin (multichain, multiligand complex):