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Exercises for the RCSB Protein Data Bank
(Version 5, 2009)
You can choose to do these using the questions as your only
guide—or see the following pages for the
step-by-step checklist to finding these answers.
1) Find out which structure the PDB ID “1cdw” denotes, where this structure was first
published and what the molecule does. What is the molecular composition of this
structure? Which functional and structural classifications does it belong to? What host
species was used to clone this gene? Look at some images of this structure.
Skills: Basic Search by PDB ID Number; Simple Information Gathering; Understanding the
Structure Summary Page; Basic Visualization Techniques.
2) How many structures of TATA-Box Binding Proteins have been resolved from humans
only (hint: use Boolean Operators)? Conduct a second search to look for TBPs that have
been resolved from species other than humans. How many did you find and what was the
range of species represented? Go to the structure summary page of Methanococcus
jannaschii TBP (2Z8U) and find details of the crystallization experiments, including the
diffraction source.
Skills: Keyword Search with Boolean Operators; Retrieving Data; Understanding Results; Structure
Summary Page Reports.
3) Were there many TBP protein structures deposited after January 1996 (hint: use
Advanced Searching options)? Look for the human structure which has the highest
resolution. How many of each type of secondary structures does this protein have?
Which class of proteins is TBP a member of? Customize the structure summary page so
that the derived data section is at the top.
Skills: Advanced Searching; Understanding & Sorting Results; Using Links; Secondary Structure
Information; Protein Classifications; Customizing the Structure Summary Page.
RCSB Protein Data Bank Exercises, version 5.
Correspond to the data available in January 2010
The materials and slides offered are for non-commercial use only. Reproduction,
distribution and/or use for commercial purposes are strictly prohibited.
Copyright 2009, OpenHelix, LLC.
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Step-by-Step checklist/instructions for the RCSB Protein Data
Bank introduction exercises
1) Find out which structure the PDB ID “1cdw” denotes, where this structure was
first published and what the molecule does. What is the molecular composition of
this structure? Which functional and structural classifications does it belong to?
What host species was used to clone this gene? Look at some images of this
structure.
Step Action
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Go to www.pdb.org, locate the Search query box on the top navigation
bar. Leave the default search type as “PDB ID or keyword” and type in
the PDB ID 1cdw.
Click on the Search button.
Note that you can also hit ‘enter’ on your keyboard.
On the Structure Summary page that you are taken to, look at the title.
Note that this structure is Human TBP (TATA-Box Binding Protein) core
domain complexed with DNA.
Find the primary citation to learn where and when this structure was
first published and to get links directly to the PubMed abstract and
PubMed Central full text article.
Note that the structure was published by Nikolov et al., in the
Proceedings of the National Academy of Science in 1996.
Scroll down to the Molecular Description section to find out how
many molecules are in this structure and what they are.
Note that there are 2 DNA molecules in this structure (16-base-pair
pieces of DNA that contain a TATA box) and a 179 amino acid
polypeptide (the TATA Binding Protein, or TBP).
Locate the Classification information at the top of the Molecular
Description section to find out what the protein component of this
structure does, in broad functional terms.
Note that this protein is involved in DNA Transcription.
Read the Source section to find the species that this protein is
normally found in and the expression system host species.
Note that it is a human protein and that E. coli was used as an
expression system. You may also want to explore the following Derived
Data section to learn about SCOP, CATH and PFAM classifications, and
associated GO terminology.
Click on “View in Jmol”, underneath the image on the top right hand of
the Structure Summary page.
Rotate the interactive image and examine it to see how clearly you
can differentiate between the DNA and protein components.
Note that right clicking on the interactive image gives viewing options.
Notes:
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2) How many structures of TATA-Box Binding Proteins have been resolved from
humans only (hint: use Boolean Operators)? Conduct a second search to look for
TBPs that have been resolved from species other than humans. How many did you
find and what was the range of species represented? Go to the structure summary
page of Methanococcus jannaschii TBP (2Z8U) and find details of the crystallization
experiments, including the diffraction source.
Step Action
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Go to www.pdb.org, and locate the Search query box on the top
navigation bar.
Leave the default search type as “PDB ID or keyword” and type
TBP AND human in the Search query box.
Note that Boolean search combinations can be achieved using
AND, OR and NOT as well as a few other terms. Also note that you
do not need to use quotes for these terms.
Click on the Search button.
Note that a results page will open with several hits shown.
Look at the top result tabs to see how many hits you found in
various categories. Scroll down to read some of the titles in
your structure results category (this is shown by default).
Note that we found 15 TBP protein structures currently, but that will
certainly change over time. Some of these are not human (like
1NH2) because the structure was annotated with the word “human”
some place, and so it was picked up by this search.
Return back to the top query box, type in TBP NOT human and
click on the Search button.
Note that you can also select the “Modify/Refine Query” from the
upper right “Query Options” menu to be taken to the Advanced
Search query form that you could also use to perform this action.
Look at the top result tabs to see many hits you got. Scroll down
to see the range of species by browsing through the titles.
Note that you have found many more structures with this query.
Note the wide range of species, including yeast and Drosophila.
Click on entry 2Z8U to go to the structure summary page of
Methanococcus jannaschii TPB.
Select the Methods report tab at the top of the summary page.
Note that you can also find some experimental details in the bottom
right Experimental Details section on the structure summary page,
but the Materials and Methods page provides many more.
Scroll down to the Diffraction section and read through it.
Note that the diffraction source is synchrotron. You can mouse over
any of the headers to be taken to a definition and also utilize the
top right options to display, download, print or share this file.
Notes:
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3) Were there many TBP protein structures deposited after January 1996 (hint: use
Advanced Searching options)? Look for the human structure which has the highest
resolution. How many of each type of secondary structures does this protein have?
Which class of proteins is TBP a member of? Customize the structure summary
page so that the derived data section is at the top.
Step Action
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Go to www.pdb.org, and click on the Advanced Search link in the left
navigation bar in the Search category.
You can also access the Advanced Search from the top right link.
From the Choose a Query Type dropdown menu, find the Structure
Annotation section and choose a Structure Title query.
Select Contains from the first dropdown menu and Type TBP in the query
box to the right of it.
Click on the Add Search Criteria to open a second query box.
From the Choose a Query Type dropdown menu, choose the Deposit Date
from the Deposition section.
Enter 1996-01-01 for the first date, and for the second date select today’s
date from the calendar by clicking on the box next to the query input box,
and then clicking on the box highlighted with today’s date.
Click on Submit Query.
Note that currently there are more than 40 results shown.
Click to open the Sort by menu on the top right of the page, and select
the Resolution option. Scroll through the list of hits you obtained and
look at the resolution of the crystals in Angstroms.
Note that the list of results is resorted from lowest Angstroms to highest.
Click on the human TBP PDB ID with the highest resolution (lowest
Angstroms), for example select 1QNA at 1.80 A.
Click on the Sequence tab at the top of its structure summary page, and
look at the secondary structure information.
Count how many alpha helices and extended strands there are.
Note that you see 4 alpha helices and 12 beta strands and you can mouse
over them to get a description.
Now go back to the Structure Summary page either by clicking on the tab
or the back button of your browser.
Towards the bottom of the Structure Summary page, open the SCOP
classifications in the Derived Data section to get information on the
family, superfamily, fold and class of this protein.
Note that TBP is a member of the alpha-beta proteins class.
Click and drag the Derived Data section to the top of the page.
Note that your page layout preferences will be saved until you select Reset
Layout at the bottom of the page to return to default.
You can also customize the homepage in a similar fashion.
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