<p>When i started programming against PDB i had a mixture of confusion &amp; frustration with the fact that certain <code>cif</code> files contain two actual structures aka assemblies of the object; i take it for granted now.</p>
<p>However, i observe now (from years of usage) that in the case of the ribosome XRAY/NMR structs frequently have exactly 2 structures aka assemblies stuck together with very little differnce between those two assemblies (~2-3 atom difference in a ~150,000 atom structure). Is there a reason for that? Does it have to do with the way microscopy is done or is it just the artifact of the deposition process? Why not deposit them as separate structures or just one if they are near nigh identical?</p>
<p>Example is <code>4V5D</code> with 2 assemblies: <a href="https://data.rcsb.org/graphql/index.html?query=%7B%0A%20%20entry(entry_id%3A%224v5d%22)%7B%0A%20%20%20%20assemblies%7B%0A%20%20%20%20%20%20rcsb_assembly_info%20%7B%0A%20%20%20%20%20%20%20%20assembly_id%0A%20%20%20%20%20%20%20%20atom_count%0A%20%20%20%20%20%20%20%20branched_atom_count%0A%20%20%20%20%20%20%20%20branched_entity_count%0A%20%20%20%20%20%20%20%20branched_entity_instance_count%0A%20%20%20%20%20%20%20%20hydrogen_atom_count%0A%20%20%20%20%20%20%20%20modeled_polymer_monomer_count%0A%20%20%20%20%20%20%20%20na_polymer_entity_types%0A%20%20%20%20%20%20%20%20nonpolymer_atom_count%0A%20%20%20%20%20%20%20%20nonpolymer_entity_count%0A%20%20%20%20%20%20%20%20nonpolymer_entity_instance_count%0A%20%20%20%20%20%20%20%20num_heterologous_interface_entities%0A%20%20%20%20%20%20%20%20num_heteromeric_interface_entities%0A%20%20%20%20%20%20%20%20num_homomeric_interface_entities%0A%20%20%20%20%20%20%20%20num_interface_entities%0A%20%20%20%20%20%20%20%20num_interfaces%0A%20%20%20%20%20%20%20%20num_isologous_interface_entities%0A%20%20%20%20%20%20%20%20num_na_interface_entities%0A%20%20%20%20%20%20%20%20num_prot_na_interface_entities%0A%20%20%20%20%20%20%20%20num_protein_interface_entities%0A%20%20%20%20%20%20%20%20polymer_atom_count%0A%20%20%20%20%20%20%20%20polymer_composition%0A%20%20%20%20%20%20%20%20polymer_entity_count%0A%20%20%20%20%20%20%20%20polymer_entity_count_DNA%0A%20%20%20%20%20%20%20%20polymer_entity_count_RNA%0A%20%20%20%20%20%20%20%20polymer_entity_count_nucleic_acid%0A%20%20%20%20%20%20%20%20polymer_entity_count_nucleic_acid_hybrid%0A%20%20%20%20%20%20%20%20polymer_entity_count_protein%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count_DNA%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count_RNA%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count_nucleic_acid%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count_nucleic_acid_hybrid%0A%20%20%20%20%20%20%20%20polymer_entity_instance_count_protein%0A%20%20%20%20%20%20%20%20polymer_monomer_count%0A%20%20%20%20%20%20%20%20selected_polymer_entity_types%0A%20%20%20%20%20%20%20%20solvent_atom_count%0A%20%20%20%20%20%20%20%20solvent_entity_count%0A%20%20%20%20%20%20%20%20solvent_entity_instance_count%0A%20%20%20%20%20%20%20%20total_assembly_buried_surface_area%0A%20%20%20%20%20%20%20%20total_number_interface_residues%0A%20%20%20%20%20%20%20%20unmodeled_polymer_monomer_count%0A%20%20%20%20%20%20%7D%0A%20%20%20%20%7D%0A%20%20%7D%0A%7D" rel="nofollow noreferrer">Assemblies data.</a></p>
<p>PS.
The relevant gql snippet for rcsb data api:</p>
<pre><code>{
  entry(entry_id:&quot;4v5d&quot;){
    assemblies{
      rcsb_assembly_info {
        assembly_id
        atom_count
        branched_atom_count
        branched_entity_count
        branched_entity_instance_count
        hydrogen_atom_count
        modeled_polymer_monomer_count
        na_polymer_entity_types
        nonpolymer_atom_count
        nonpolymer_entity_count
        nonpolymer_entity_instance_count
        num_heterologous_interface_entities
        num_heteromeric_interface_entities
        num_homomeric_interface_entities
        num_interface_entities
        num_interfaces
        num_isologous_interface_entities
        num_na_interface_entities
        num_prot_na_interface_entities
        num_protein_interface_entities
        polymer_atom_count
        polymer_composition
        polymer_entity_count
        polymer_entity_count_DNA
        polymer_entity_count_RNA
        polymer_entity_count_nucleic_acid
        polymer_entity_count_nucleic_acid_hybrid
        polymer_entity_count_protein
        polymer_entity_instance_count
        polymer_entity_instance_count_DNA
        polymer_entity_instance_count_RNA
        polymer_entity_instance_count_nucleic_acid
        polymer_entity_instance_count_nucleic_acid_hybrid
        polymer_entity_instance_count_protein
        polymer_monomer_count
        selected_polymer_entity_types
        solvent_atom_count
        solvent_entity_count
        solvent_entity_instance_count
        total_assembly_buried_surface_area
        total_number_interface_residues
        unmodeled_polymer_monomer_count
      }
    }
  }
}
</code></pre>

CC BY-SA 4.0
2023-02-23T11:00:56.303Z
..... Refinement was conducted using CNS first through a rigid body refinement of each of the two 70S molecules in the asymmetric unit; an additional rigid body refinement where each domain of the ribosome, the tRNAs and ribosomal proteins were defined as separate rigid-body groups, followed by two rounds of energy minimization and B-factor refinement. .... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679717/
pippo1980
CC BY-SA 4.0
2023-02-23T11:02:02.683Z
PS your graphql link returns an error
pippo1980
CC BY-SA 4.0
2023-02-23T23:05:15.017Z
@pippo1980 i see, that's how they processed it. Still begs the question why they refine two molecules together and why they deposit it together. Basically every xray structure of the ribosome in PDB is like that... Is it just that it's infeasible to separate them before the X-ray..?
rtviii
CC BY-SA 4.0
2023-02-24T06:38:03.013Z
I remember about xray, dont know much about cryoEM but: The content of the asymmetric unit depends on the crystallized molecule's position(s) and its conformations within the unit cell. Depending on the crystallization conditions and local packing two distinct scenarios may occur: Copies of the macromolecule or complex within a crystal unit cell have identical conformations and occupy symmetry-related positions.
pippo1980
CC BY-SA 4.0
2023-02-24T06:38:24.110Z
As a result, the biological assembly may either be composed of one copy of the macromolecule/complex or it may be composed of two or more symmetry related molecules/complexes coming together to form a larger assembly.
Copies of the macromolecule or complex take on slightly different conformations and occupy unique positions in the crystal asymmetric unit. As a result, each of the different positions of the macromolecule/complex may correspond to structurally similar but not identical biological assemblies.
pippo1980
CC BY-SA 4.0
2023-02-24T06:39:08.393Z
see https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies , I believe nowadays all the molecules present into the AU are shipped in the cif
pippo1980
CC BY-SA 4.0
2023-02-24T06:45:43.147Z
interesting too https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157440/ Molecular replacement with a large number of molecules in the asymmetric unit
pippo1980
CC BY-SA 4.0
2023-02-25T03:54:13.080Z
Thanks for carrying on the conversation, @pippo1980. I hope we are not talking past each other, but i get the AU and it's flexible relationship to the assembly. My question in the pdb lingo, i guess, is mostly along the lines of "why is it that every XRAY ribosome is an assymetric unit with multiple biological assemblies" i.e. case 3 in the pdb101 article u link. Why not 1000s like nmr (disk-space notwithstanding) or varying numbers of assemblies(some 2, some 14, some 1, some X..) between depositions? It is always two assemblies. Leads me to think it's experimental.
rtviii
CC BY-SA 4.0
2023-02-25T11:24:43.630Z
NMR is another world, molecule in solution moves so thats why you get all the conformation you can see in the different models, didnt know the reach the ability to get ribosome assemblies by NMR. Still cant get your question, hope somebody else could jump in, maybe I am missing something
pippo1980
CC BY-SA 4.0
2023-02-25T20:18:00.603Z
Thanks a lot anyway!
rtviii
<protein-structure><assembly><pdb><ribosomal>
Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
# Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?

(Asked by: username_0 on 2023-02-22)

When i started programming against PDB i had a mixture of confusion & frustration with the fact that certain cif files contain two actual structures aka assemblies of the object; i take it for granted now.
However, i observe now (from years of usage) that in the case of the ribosome XRAY/NMR structs frequently have exactly 2 structures aka assemblies stuck together with very little differnce between those two assemblies (~2-3 atom difference in a ~150,000 atom structure). Is there a reason for that? Does it have to do with the way microscopy is done or is it just the artifact of the deposition process? Why not deposit them as separate structures or just one if they are near nigh identical?
Example is 4V5D with 2 assemblies: Assemblies data.
PS.
The relevant gql snippet for rcsb data api:
{
  entry(entry_id:"4v5d"){
    assemblies{
      rcsb_assembly_info {
        assembly_id
        atom_count
        branched_atom_count
        branched_entity_count
        branched_entity_instance_count
        hydrogen_atom_count
        modeled_polymer_monomer_count
        na_polymer_entity_types
        nonpolymer_atom_count
        nonpolymer_entity_count
        nonpolymer_entity_instance_count
        num_heterologous_interface_entities
        num_heteromeric_interface_entities
        num_homomeric_interface_entities
        num_interface_entities
        num_interfaces
        num_isologous_interface_entities
        num_na_interface_entities
        num_prot_na_interface_entities
        num_protein_interface_entities
        polymer_atom_count
        polymer_composition
        polymer_entity_count
        polymer_entity_count_DNA
        polymer_entity_count_RNA
        polymer_entity_count_nucleic_acid
        polymer_entity_count_nucleic_acid_hybrid
        polymer_entity_count_protein
        polymer_entity_instance_count
        polymer_entity_instance_count_DNA
        polymer_entity_instance_count_RNA
        polymer_entity_instance_count_nucleic_acid
        polymer_entity_instance_count_nucleic_acid_hybrid
        polymer_entity_instance_count_protein
        polymer_monomer_count
        selected_polymer_entity_types
        solvent_atom_count
        solvent_entity_count
        solvent_entity_instance_count
        total_assembly_buried_surface_area
        total_number_interface_residues
        unmodeled_polymer_monomer_count
      }
    }
  }
}

**Tags:** protein-structure, assembly, pdb, ribosomal
> **Comments:**
> **username_1**: ..... Refinement was conducted using CNS first through a rigid body refinement of each of the two 70S molecules in the asymmetric unit; an additional rigid body refinement where each domain of the ribosome, the tRNAs and ribosomal proteins were defined as separate rigid-body groups, followed by two rounds of energy minimization and B-factor refinement. .... https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679717/  
> **username_1**: PS your graphql link returns an error  
> **username_0**: @pippo1980 i see, that's how they processed it. Still begs the question why they refine two molecules together and why they deposit it together. Basically every xray structure of the ribosome in PDB is like that... Is it just that it's infeasible to separate them before the X-ray..?  
> **username_1**: I remember about xray, dont know much about cryoEM but: The content of the asymmetric unit depends on the crystallized molecule's position(s) and its conformations within the unit cell. Depending on the crystallization conditions and local packing two distinct scenarios may occur: Copies of the macromolecule or complex within a crystal unit cell have identical conformations and occupy symmetry-related positions.  
> **username_1**: As a result, the biological assembly may either be composed of one copy of the macromolecule/complex or it may be composed of two or more symmetry related molecules/complexes coming together to form a larger assembly. Copies of the macromolecule or complex take on slightly different conformations and occupy unique positions in the crystal asymmetric unit. As a result, each of the different positions of the macromolecule/complex may correspond to structurally similar but not identical biological assemblies.  
> **username_1**: see https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/biological-assemblies , I believe nowadays all the molecules present into the AU are shipped in the cif  
> **username_1**: interesting too https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157440/ Molecular replacement with a large number of molecules in the asymmetric unit  
> **username_0**: Thanks for carrying on the conversation, @pippo1980. I hope we are not talking past each other, but i get the AU and it's flexible relationship to the assembly. My question in the pdb lingo, i guess, is mostly along the lines of "why is it that every XRAY ribosome is an assymetric unit with multiple biological assemblies" i.e. case 3 in the pdb101 article u link. Why not 1000s like nmr (disk-space notwithstanding) or varying numbers of assemblies(some 2, some 14, some 1, some X..) between depositions? It is always two assemblies. Leads me to think it's experimental.  
> **username_1**: NMR is another world, molecule in solution moves so thats why you get all the conformation you can see in the different models, didnt know the reach the ability to get ribosome assemblies by NMR. Still cant get your question, hope somebody else could jump in, maybe I am missing something  
> **username_0**: Thanks a lot anyway!  

---

## 0 answers

