Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-23T11:00:56.303Z
Comments.Text: ..... 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/
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-23T11:02:02.683Z
Comments.Text: PS your graphql link returns an error
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-23T23:05:15.017Z
Comments.Text: @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..?
Comments.UserDisplayName: rtviii
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-24T06:38:03.013Z
Comments.Text: 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.
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-24T06:38:24.110Z
Comments.Text: 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.
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-24T06:39:08.393Z
Comments.Text: 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
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-24T06:45:43.147Z
Comments.Text: interesting too https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157440/ Molecular replacement with a large number of molecules in the asymmetric unit
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-25T03:54:13.080Z
Comments.Text: 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.
Comments.UserDisplayName: rtviii
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-25T11:24:43.630Z
Comments.Text: 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
Comments.UserDisplayName: pippo1980
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-02-25T20:18:00.603Z
Comments.Text: Thanks a lot anyway!
Comments.UserDisplayName: rtviii
Tags: <protein-structure><assembly><pdb><ribosomal>
Title: Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
ThreadText: # 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.](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)
  
  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**: @username_1 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, @username_1. 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
  
  