1. SUMMARY: PDB 1TJA EMD 1086 [and EMD 1089]1TJA10861089 (examples 1 and 2 from Oct 2004 cryo-em workshop)Oct 2004 cryo-em workshop T4 bacteriophage after treatment with urea

2. What has been done Comparison of coordinates and map (Chimera). Comparison of PDB cif file items with EMD xml file items and vice versa. Thinking about likely complexities of future depositions—focus on entity/assembly related issues.

3. Major Findings The following images show that 1tja is in the same reference frame as emd1086, but not in the same reference frame as emd1089. ***Followup with deposition authors (1/11/05) has confirmed that 1tja coordinates are fitted to emd1086, NOT to emd1089***.

4. Image: 1TJA-EMD1089 and EMD1086 EMD1086 PDB1TJA EMD1089 Image made with Chimera

5. Image: 1TJA-EMD1089 PDB1TJA EMD1089 Image made with Chimera

6. Major Findings, cont’d. In most cases (not quite all), corresponding data items between 1tja and em1086 match. Items Collected By EMDB Items Collected By PDB Items collected by Both

7. Major Findings, cont’d. Confusion about how to properly fill in assembly-related cif items.

8. CIF: higher level structure em_entity_assembly _em_entity_assembly.id _em_entity_assembly.assembly_id _em_entity_assembly.type _em_entity_assembly.name _em_entity_assembly.details _em_entity_assembly.ebi_organism_scientific _em_entity_assembly.ebi_organism_common _em_entity_assembly.ebi_strain _em_entity_assembly.ebi_tissue _em_entity_assembly.ebi_cell _em_entity_assembly.ebi_organelle _em_entity_assembly.ebi_cellular_location _em_entity_assembly.ebi_engineered _em_entity_assembly.ebi_expression_system _em_entity_assembly.ebi_expression_system_plasmid _em_entity_assembly.go_id _em_entity_assembly.ipr_id _em_entity_assembly.synonym em_entity_assembly_list _em_entity_assembly_list.id _em_entity_assembly_list.entity_id _em_entity_assembly_list.entity_assembly_id _em_entity_assembly_list.details _em_entity_assembly_list.number_of_copies em_assembly _em_assembly.id _em_assembly.entry_id _em_assembly.name _em_assembly.aggregation_state _em_assembly.composition _em_assembly.num_components _em_assembly.mol_wt_exp _em_assembly.mol_wt_theo _em_assembly.mol_wt_method _em_assembly.details (based on Dictionary before Oct 2004)

9. EM_Assembly Data items in the EM_ASSEMBLY category record details about the type of complex assembly that describes the nature of the sample studied. Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex. Data items in the EM_ENTITY_ASSEMBLY_LIST category record details of the structural elements in each component.

10. T4 bacteriophage Source: http://news.uns.purdue.edu/UNS/newspix03/pix644.html

11. more detail Source: Leiman et al., Cell. Mol. Life Sci 60 (2003), 2356-2370.