Copyright OpenHelix. No use or reproduction without express written consent1
Materials prepared by: Sawsan Khuri, Ph.D. and Cynthia Perreault-Micale, Ph.D. Updated: Q Version 7 The RCSB Protein Data Bank
Copyright OpenHelix. No use or reproduction without express written consent3 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
URL Organisms Copyright OpenHelix. No use or reproduction without express written consent4 Introduction & Credits: RCSB PDB to Access: Molecule of the Month Experimental Data Structure Comparisons MyPDB Alerts Many Tools and Resources The RCSB PDB is managed by 2 members of RCSB
Copyright OpenHelix. No use or reproduction without express written consent5 RCSB PDB Features: widget framework for customized displays Drag areas to desired location help menu Drag areas to desired location
click Copyright OpenHelix. No use or reproduction without express written consent6 Help System: POP-OUT or Use & CLOSE Use help system in 2 nd window, or “over” current page Search help, then close to return to RCSB PDB
Structure Deposition & Unique PDB Identifiers Copyright OpenHelix. No use or reproduction without express written consent7 PDB ID examples: 2ara 1lr5 1e5s Proline hydroxylase Auxin Binding Protein AraC transcription factor (not case-sensitive)
Copyright OpenHelix. No use or reproduction without express written consent8 An Example of a Structure Summary Page β-strands α-helices Biological Assembly – 2 asymmetric units sugar-binding domains loops
Copyright OpenHelix. No use or reproduction without express written consent9 More Background Information Link at bottom of homepage
Copyright OpenHelix. No use or reproduction without express written consent10 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
RCSB PDB Homepage Copyright OpenHelix. No use or reproduction without express written consent11 Top bar search To links & options News area Featured Molecule Featured System Drillable Data Distribution Summaries Latest Structures Header Browse Or Advanced search
Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent12 Search Categories and examples: All Categories: e.g. PDB ID; molecule name; author Author: e.g. Perutz, MF; smith, j Macromolecule: e.g. Prothrombin; histone Sequence: e.g. vpstaireisllkelkddnivrlydivhsdahk Ligand: e.g. biotin, BTN Additional search options options
Copyright OpenHelix. No use or reproduction without express written consent13 All Categories for Transcription Factor Information click Our Query = Transcription factor p65 click
Copyright OpenHelix. No use or reproduction without express written consent14 Data Distribution Results Data distribution of hits Molecules of the Month Table of results enlarge Advanced search Save search Query details, including Query in XML format
Copyright OpenHelix. No use or reproduction without express written consent15 Search Results Data distribution of hits Molecules of the Month Table of results enlarge Special education features related to query terms List of resulting structures Hyperlinked text Result Options: - Download - view PDB file - structure visualization Display options
Search Categories and examples: All Categories: e.g. PDB ID; molecule name; author Author: e.g. Perutz, MF; smith, j Macromolecule: e.g. Prothrombin; histone Sequence: e.g. vpstaireisllkelkddnivrlydivhsdahk Ligand: e.g. biotin, BTN Additional search options Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent16 click Input PDB ID & chain ID or paste Sequence (Protein or nucleotide) Search methods BLAST vs. FASTA: See RCSB PDB Help or OpenHelix tutorials
Top Search Bar: Multiple Search Categories Copyright OpenHelix. No use or reproduction without express written consent17 Search options click
Copyright OpenHelix. No use or reproduction without express written consent18 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
Copyright OpenHelix. No use or reproduction without express written consent19 Summary Page Primary Citation One for every structure Organized similarly It provides access to a wealth of data Customizable with a widget framework Re-arranged sections in red Use Reset Layout to return to default Source Ligand Component Experiment Details Deposition Summary Images & Viewing Options Menus Related Entries 2arc Enter 2arc External Data (orange) MyPDB Molecular Description Report tabs Title & ID Images & Viewing Options Molecular Description Primary Citation Source Ligand Component Related Entries External Data (orange) Experiment Details Deposition Summary MyPDB Report tabs Title & ID Menus Reset Layout
Copyright OpenHelix. No use or reproduction without express written consent20 Structure Summary Page - Top AraC AND L-arabinose citation reports Title & ID
Copyright OpenHelix. No use or reproduction without express written consent21 Structure Summary Page – Top, cont. Larger image “Looking at Structures” Education section Toggle through views Click here Asymmetric Unit options:
Copyright OpenHelix. No use or reproduction without express written consent22 Jmol Viewer Mouse over for info & click to display Help tab Scripting box Right click Menus to easily change coloring & display styles
Copyright OpenHelix. No use or reproduction without express written consent23 Structure Summary Page - Bottom Source Related PDB Entries Ligand Component External Annotations MyPDB Deposition Summary Experimental Details
Ligand Chemical Component - Ligand Explorer Copyright OpenHelix. No use or reproduction without express written consent24
Copyright OpenHelix. No use or reproduction without express written consent25 Sequence Tab Graphic of secondary structures Choose domain assignments or annotations from dropdown menu Specify how you want to view graphic Results Tabs Select more annotations References below Set viewing preferences submit
Copyright OpenHelix. No use or reproduction without express written consent26 Annotations Report Database links CATH SCOP PFAM SBKB
Copyright OpenHelix. No use or reproduction without express written consent27 Sequence Similarity Report
Copyright OpenHelix. No use or reproduction without express written consent28 3D Similarity Report Alignment summary Jmol viewer Toggle alignment views Block Conservation Other comparison methods Download & Help
Copyright OpenHelix. No use or reproduction without express written consent29 Literature Report Additional PDB entries
Copyright OpenHelix. No use or reproduction without express written consent30 Mouse over for details Biology & Chemistry Report Structure Details Protein Details Gene Details
Copyright OpenHelix. No use or reproduction without express written consent31 Methods Report Details vary by protein, can include: Crystallization Crystal data Diffraction Refinement data Refinement Software & computing Crystallization Diffraction More sections Crystal data
Copyright OpenHelix. No use or reproduction without express written consent32 Color- coded Geometry Report Top Details of bond lengths & angles Middle Lower
Copyright OpenHelix. No use or reproduction without express written consent33 Geometry Report Bond Length Table
Copyright OpenHelix. No use or reproduction without express written consent34 Links Report Scroll down to SCOP & CATH
Copyright OpenHelix. No use or reproduction without express written consent35 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
Copyright OpenHelix. No use or reproduction without express written consent36 Additional Homepage Features Next slide RCSB PDB statistics & growth Browse term hierarchies, See associated structures
Copyright OpenHelix. No use or reproduction without express written consent37 Advanced Search Form keyword Build elegant, multi-faceted queries Add criteria
Copyright OpenHelix. No use or reproduction without express written consent38 Advanced Search Example, Criteria 1 Molecule type Change defaults from “ignore” click
Copyright OpenHelix. No use or reproduction without express written consent39 Advanced Search Example, Criteria 2 Experimental Method X-RAY Yes Any = “OR”
Copyright OpenHelix. No use or reproduction without express written consent40 Advanced Search Example, Additional Criteria menus # of Entities Has Ligand(s) 5 5
Copyright OpenHelix. No use or reproduction without express written consent41 Advanced Search Results Our query PDB Advanced searches = powerful data access tool
Copyright OpenHelix. No use or reproduction without express written consent42 Additional Homepage Features, cont.
Copyright OpenHelix. No use or reproduction without express written consent43 Latest Release New structure Papers Additional Homepage Features, New Structures Lower on page, FTP archive access
Copyright OpenHelix. No use or reproduction without express written consent44 Unreleased Entries Search Query specific structures
Copyright OpenHelix. No use or reproduction without express written consent45 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
Click on Compare Structures FTP services Copyright OpenHelix. No use or reproduction without express written consent46 Tools & Educational Resources
Copyright OpenHelix. No use or reproduction without express written consent47 The RCSB PDB Comparison Tool To Expert mode - vary parameters Read more Sequence Structure Example
Copyright OpenHelix. No use or reproduction without express written consent48 PDB-101: Structural View of Biology “Life is three- dimensional. … PDB-101 offers tools to explore the molecules of biological processes that define life.” Drillable subcategories
Copyright OpenHelix. No use or reproduction without express written consent49 Navigate to specific topics Detailed introduction and tips for new PDB users PDB-101: Understanding PDB Data
Copyright OpenHelix. No use or reproduction without express written consent50 PDB-101: Molecule of the Month Full report click to expand topic
Copyright OpenHelix. No use or reproduction without express written consent51 PDB-101: Educational Resources Available Materials: Posters/Exhibits Website tutorials Animations Activities/lessons Events
Copyright OpenHelix. No use or reproduction without express written consent52 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
Copyright OpenHelix. No use or reproduction without express written consent53 Summary Intuitive searches Customizable views Tools PDB-101 For education Featured Molecules Drillable data summaries
Copyright OpenHelix. No use or reproduction without express written consent54 Summary, cont Topic reports Structure Summary Report
Copyright OpenHelix. No use or reproduction without express written consent55 RCSB Protein Data Bank Agenda Introduction & Credits Top Search Bar & Results Structure Summary Page More Homepage Features Tools & Education Summary Exercises RCSB PDB:
Copyright OpenHelix. No use or reproduction without express written consent56