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RNA Polymerase II
St. Dominic Middle School Smart Team
18105 W. Capitol Drive, Brookfield ,WI 53045
This is RNA Polymerase II with 10 of its 12 subunits. This model
shows how the DNA and RNA fit inside the enzyme for the
transcription process. The DNA is cyan and the RNA is
magenta. The bridge helix is the green structure in the picture.
The bridge helix moves the DNA along to be transcribed. The
black spot is the magnesium ion in the active site, which adds
nucleotides to the growing RNA transcript. The clamp (orange)
swings over the DNA to hold it down to be transcribed.
Clamp
RNA Polymerase II (Pol II), a major up-keeper of our cells, is found
in the nucleus of all eukaryotic cells and is one of the most
important enzymes in our body. Pol II has twelve protein subunits,
which also makes it one of the largest molecules. Its function is to
surround the DNA, unwind it, separate it into two strands, and use
the DNA template strand to create a messenger RNA (mRNA) copy
of a gene. These mRNA copies of genes are needed by the cell to
make proteins to keep the cell healthy. The mRNAs are the
templates used by ribosomes to link amino acids into long chains in
the correct order to form all the different proteins in our bodies. In
fact, RNA Pol II is so essential to life that when the poison, αamanitin, from the Death Cap mushroom attaches to RNA Pol II,
death occurs within 10 days. The α-amanitin goes into the funnel
portion of Pol II and inserts under the bridge helix. The poison is
thought to limit the movement of the bridge helix and prevent a
ratcheting movement that translocates the DNA template. When
working properly, RNA Pol II can make RNA copies of DNA at
speeds of about 3600 bases per minute. The α-amanitin slows this
speed to 2 or 3 bases per minute. At this slow speed, RNA
Polymerase II cannot do its job of making messenger RNA copies
of our genes. Without mRNA molecules, the ribosomes cannot
make the thousands of different proteins needed for life.
Lid
Zipper
Rudder
Chain A
Chain A
Chain A
First Amino Acid
Bridge Helix
Last Amino Acid
Magnesium Ion
DNA Template
RNA Transcript
Chain A is the largest subunit of RNA Polymerase II. RNA Polymerase II makes a copy of the DNA, called
messenger RNA, using the template strand. The DNA is unwound by RNA Pol II as it enters the enzyme.
The clamp then closes over the DNA after it has been unwound. Movement of the bridge helix is thought to
translocate the DNA so that nucleotides can be added to the RNA transcript. The rudder separates DNA and
RNA from each other and the lid then guides mRNA and DNA template out of the enzyme. Finally, the zipper
joins the DNA template strand to the non-template strand.
Students:
Sam Andreski, Julie Armstrong, Greg Cigich,
Andrew Cobb, Kevin Drees, Mark Engel, Matt
Geisinger, Joe Heckes, Patrick Jordan, Ryan
Kohl, Kevin Koprowski, Michael Moakley,
Rachael Reit, Tara Robey, Andrew Ruka,
Michael Russell, Lauren Schmidt, Tyler
Sherman, Paige Siehr
Teacher: Donna LaFlamme
Scientist Mentor: Dr. Vaughn Jackson,
Medical College of Wisconsin
RNA Polymerase II
Coding Strand
Double
stranded
DNA
A T G T C T A G A T A G
A T G T C T A G A T A G
T A C A G A T C T A T C
A U G U C U
T A C A G A T C T A T
Messenger RNA
C
Template Strand
Our three-dimensional model of RNA Polymerase II
was made by the Z-Corp printer.
The Z-Corp printer is a printer
that can print out threeA T G T C T A G A T A G
dimensional designs, in millions
of colors, from programs like
T A C A G A T C T A T C
RasMol. RasMol is a program
that can be used to view structure files deposited by
This is the process of transcription. The RNA Polymerase II (green) comes and separates the strands of
scientists in the Protein Data Bank. The Z-Corp
DNA. It then adds the nucleotide bases A, U, C, or G that compliment the template strand of DNA to
prints in three dimensions by using layers of plaster
make messenger RNA. When the RNA Pol II is finished, the mRNA copy floats away and the DNA gets
instead of paper. To make the model, the printer
zipped back together. The mRNA floats out into the cytoplasm to attach to a ribosome and be translated
keeps adding layers of plaster from a moving boom.
into a protein.
The boom then repeatedly adds color and glue to
areas on the surface indicated by a script file.
Supported by the National Institutes of Health (NIH) – National Center for Research Resources Science Education Partnership
Partnership Award (NCRR(NCRR-SEPA)
A U G U C U A G A U A G
Primary Citation: Structural Basis of Transcription: An RNA
Polymerase II Elongation Complex at 3.3 Angstrom Resolution,
Averell L. Gnatt, Patrick Cramer, Jianhua Fu, David A. Bushnell,
Roger D. Kornberg, Science, Volume 292, page 1876
This figure was adapted from the article Structural
Basis of Transcription: α-Amanitin-RNA
Polymerase II Cocrystal at 2.8 angstrom
resolution, David A. Bushnell, Patrick Cramer,
and Roger D. Kornberg, PNAS, online Jan. 22,
2002