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Visualization of Large Biomolecular Complexes

Visualization of Large Biomolecular Complexes. Cathy Lawson RCSB-PDB, Rutgers University Visualization Workshop @ SDSC September 2005. Growth of Coordinate Entries. Number of released coordinate entries. Year. Growth of EM Entries. kelp fly virus. 150. acetylcholine receptor.

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Visualization of Large Biomolecular Complexes

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  1. Visualization of Large Biomolecular Complexes Cathy Lawson RCSB-PDB, Rutgers University Visualization Workshop @ SDSC September 2005

  2. Growth of Coordinate Entries Number of released coordinate entries Year

  3. Growth of EM Entries kelp fly virus 150 acetylcholine receptor August 2005 70S ribosome rhinovirus-receptor complex recA hexamer bacteriorhodopsin

  4. Current Challenges in RepresentingCoordinates of Large Complexes • Format • Symmetry For further info: Dutta S & Berman HM, Large macromolecular complexes in the Protein Data Bank: a status report. Structure. 2005 Mar;13(3):381-8. PMID: 15766539

  5. Coordinate Format PDB format • limited format: maximum of 99,999 atoms, 62 chains • larger structures are represented in multiple files mmCIF/PDBML formats • no restrictions on size • mmCIF recognized by many crystallography applications • use is strongly encouraged for visualization applications • more info: http://mmcif.rcsb.org/, http://pdbml.rcsb.org/ mmCIF example: loop_ _atom_site.id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_seq_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z 1 O5* G A 1 -3.897 61.994 -24.841 2 C5* G A 1 -5.016 62.932 -24.760

  6. Symmetry Asymmetric Unit  Biological Unit • Non-trivial problem to provide a correct set of transformations and a procedure for applying them • We are investigating ways to better standardize this process • Full biological units are available from the RCSB-PDB biological unit • Transformation types: • Noncrystallographic (general) • Crystallographic • Point or helical asymmetric unit Rice Dwarf Virus

  7. Current Challenges in Representing EM Maps of Large Complexes • Format • Validation

  8. Examples of Map Format Issues Map on different scale Map in different frame EMD_1060 1UF2 2BK2 EMD_1106 Rice Dwarf Virus Pneumolysin Prepore Complex

  9. Visualization Needs • Educators • Annotators • Structural Biologists

  10. Educator Needs AstexViewer (development version) • free software • open source • multiple platforms • no browser dependence • easy to install and use • user-friendly interface • Common themes from a survey of • ~25 educators world-wide • (S. Dutta, RCSB-PDB, 2003)

  11. Annotator Needs • Quick display, even for large complexes • Display secondary structure • Select atoms or residues for display or rendering • Show symmetry-related molecules • Color all or selected residues or chains • Compute distances • Display standard and unusual ligands • Support for mmCIF format • Overlay coordinates and maps (particularly for EM)

  12. Needs of a Seasoned Structural Biologist • logical menus for all common actions • command line and macros for complex actions • documentation with lots of examples • save and restart sessions • complete control over viewing parameters • multiple representation styles for biological polymers and maps • symmetry generation (crystal, point, helical) • full coordinate and map editing capabilities • import/export coordinates AND MAPS in multiple formats • 3D • movies

  13. Acknowledgements • Helen Berman • Shuchismita Dutta • Kyle Burkhardt, Jeramia Ory • Kim Henrick (EBI) Molecular Images: • RCSB-PDB molecule of the month • EMDB • VIPER • AstexViewer • rendering with Pymol , UCSF Chimera

  14. RCSB-PDB Annotator Team

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