4BY7: Elongating RNA Polymerase Ii-bye1 TLD Complex

Citation:
Abstract
Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Here we show that Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II, and report crystal structures of the Bye1 TLD bound to Pol II and three different Pol II-nucleic acid complexes. Like TFIIS, Bye1 binds with its TLD to the Pol II jaw and funnel. In contrast to TFIIS, however, it neither alters the conformation nor the in vitro functions of Pol II. In vivo, Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.
PDB ID: 4BY7Download
MMDB ID: 113350
PDB Deposition Date: 2013/7/18
Updated in MMDB: 2013/10 
Experimental Method:
x-ray diffraction
Resolution: 3.15  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4BY7: hexadecameric; determined by author and by software (PISA)
Molecular Components in 4BY7
Label Count Molecule
Proteins (13 molecules)
1
DNA-directed RNA Polymerase II Subunit Rpb1(Gene symbol: RPO21)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb3(Gene symbol: RPB3)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb2(Gene symbol: RPB2)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 1(Gene symbol: RPB5)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb4(Gene symbol: RPB4)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb7(Gene symbol: RPB7)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 2(Gene symbol: RPO26)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb9(Gene symbol: RPB9)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 3(Gene symbol: RPB8)
Molecule annotation
1
DNA-directed RNA Polymerase II Subunit Rpb11(Gene symbol: RPB11)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 5(Gene symbol: RPB10)
Molecule annotation
1
DNA-directed RNA Polymerases I, II, and III Subunit Rpabc 4(Gene symbol: RPC10)
Molecule annotation
1
Transcription Factor Bye1(Gene symbol: BYE1)
Molecule annotation
Nucleotides(3 molecules)
1
, 5'-d(*dap*ap*ap*gp*tp*ap*cp*tp*tp*gp*ap*gp*cp*dtp)-3'
Molecule annotation
1
5'-d(*dap*gp*cp*tp*cp*ap*ap*gp*tp*ap*cp*tp*tp*dap *tp*tp*cp*cp*bp*gp*gp*tp*cp*ap*tp*t)-3'
Molecule annotation
1
5'-r(*up*up*cp*gp*ap*cp*cp*ap*gp*gp*ap)-3'
Molecule annotation
Chemicals (11 molecules)
1
8
2
1
3
2
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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