HATs
HMTs
SWI/SNF
RSC
HATs
HMTs
SWI/SNF
RSC
RNA polymerase II underlies
the central dogma of molecular biology
Pol I
Pol II
Pol III
rRNA
tRNA
Ribosome
DNA mRNA Protein
RNA polymerase II transcription machinery
Pol II DNA unwinding
RNA polymerization
proofreading
GTFs
(TFIIB, -D, -E, -F, -H)
promoter recognition
Mediator of Transcriptional Regulation
• Required for all transcription of all pol II promoters
• Essential link in the chain of communication:
enhancer activator Mediator pol II promoter
• Co-activator, co-repressor, and general transcription
factor
• Processes, transduces transcriptional regulatory
information in all eukaryotes
Proteins 10
Amino acids 3559
Atoms 28,378
MW 0.5 MDa
Rfree (2.8 Å) 28.2 %
Template
Hybrid
RNA
5’
Pol II
Nontemplate
post-translocation NTP enters E site
NTP rotates into A site
pre-translocation
Trigger loop contacts NTP in the A site
Multiple conformations of the trigger loop
Trigger Loop Network
Trigger Loop Network
Nucleotide selection in
RNA chain extension from 10 to 11 residues
Trigger loop couples nucleotide selection to catalysis
His1085
20.5 Å
RNA/DNA
(Py:Py mismatch)
20.5 Å
DNA/DNA
22.5 Å
RNA/DNA
Nucleotide selection by alignment with the trigger loop,
coupling recognition to catalysis
Trigger Loop Network
-7
-8
-9
-10
3.4
4.4
5.2
12 Angstroms
Template DNA
RNA
Fork loop
Rudder
Lid
Template
RNA