Biological assembly of a structure

Often the biological assembly (or biological unit) reveals the complete picture of a protein function, may it be a viral capsid or a microfilament. However, the usual atom records in an PDB or PDBx file usually describe only the asymmetric unit. For large complexes the asymmetric unit may only display one monomer or one small subcomplex. Multiple copies of the asymmetric unit must be geometrically arranged to build the assembly.

In order to get the entire assembly, the PDBx files provided by the RCSB PDB (either in CIF or BinaryCIF format) contain the following fields:

• pdbx_struct_assembly - General information about the assemblies

• pdbx_struct_assembly_prop - More specific properties

• pdbx_struct_oper_list - A list of tranformation operations

• pdbx_struct_assembly_gen - Which tranformation operations from pdbx_struct_oper_list need to be applied for the assemblies

More information about biological assemblies is provided by the RCSB PDB on this page.

In this example, we will create the complete biological assembly of the capsid from the lambda phage.

At first we will check, which assemblies are available to us.

# Code source: Patrick Kunzmann
# License: BSD 3 clause

import biotite.database.rcsb as rcsb
import biotite.interface.pymol as pymol_interface
import biotite.structure as struc
import biotite.structure.io.pdbx as pdbx

PDB_ID = "7VII"


pdbx_file = pdbx.BinaryCIFFile.read(rcsb.fetch(PDB_ID, "bcif"))

assemblies = pdbx.list_assemblies(pdbx_file)
print("ID    name")
print()
for assembly_id, name in assemblies.items():
    print(f"{assembly_id:2}    {name}")

ID    name

1     complete icosahedral assembly
2     icosahedral asymmetric unit
3     icosahedral pentamer
4     icosahedral 23 hexamer
5     icosahedral asymmetric unit, std point frame

'complete icosahedral assembly' sounds good. In fact, often the first assembly is the complete one. Hence, the get_assembly() function builds the first assembly by default. Since we know the ID we want ('1'), we will provide it to this function anyway. It returns the chosen assembly as AtomArray. Note that the assembly ID is a string, not an integer.

assembly = pdbx.get_assembly(
    pdbx_file,
    assembly_id="1",
    model=1,
    # To identify later which atoms belong to which protein type
    extra_fields=["label_entity_id"],
)

print("Number of protein chains:", struc.get_chain_count(assembly))

Number of protein chains: 840

The assembly consists of two different protein types, so called entities. Each entity may be represented by multiple chain IDs.

entity_info = pdbx_file.block["entity"]
print("ID    description")
print()
for entity_id, description in zip(
    entity_info["id"].as_array(), entity_info["pdbx_description"].as_array()
):
    print(f"{entity_id:2}    {description}")

ID    description

 1    Major capsid protein
 2    Capsid decoration protein

Now we could do some analysis on the biological unit. But for this example we will visualize the entire assembly.

# Show capsid structure as CA spheres to increase rendering speed
assembly = assembly[assembly.atom_name == "CA"]
pymol_object = pymol_interface.PyMOLObject.from_structure(assembly)
pymol_object.color("biotite_dimgreen", assembly.label_entity_id == "1")
pymol_object.color("biotite_lightorange", assembly.label_entity_id == "2")
pymol_object.set("sphere_scale", 2.0)
pymol_object.show_as("spheres")
pymol_object.zoom(buffer=25)
pymol_interface.show((1500, 1500))

/home/runner/miniconda3/envs/test/lib/python3.12/site-packages/biotite/interface/pymol/convert.py:105: UserWarning: The given atom array (stack) has no associated bond information
  warnings.warn("The given atom array (stack) has no associated bond information")