DNA Binding Motif

Accessions: 7khi_F (3D-footprint 20231221)
Names: RNA polymerase sigma factor RpoD
Organisms: Escherichia coli, strain K12
Libraries: 3D-footprint 20231221 1
1 Contreras-Moreira B. 3D-footprint: a database for the structural analysis of protein-DNA complexes. Nucleic acids research 38:D91-7 (2010). [Pubmed]
Description: Escherichia coli RNA polymerase and rrnBP1 promoter complex with DksA/ppGpp
Length: 24
Consensus: Agnnwnnnnnnnnnnnnnnacaag
Weblogo:
PSSM: P0 A C G T
01 96 0 0 0 A
02 14 16 52 14 g
03 24 24 24 24 n
04 24 24 24 24 n
05 27 22 22 25 w
06 24 24 24 24 n
07 24 24 24 24 n
08 24 24 24 24 n
09 24 24 24 24 n
10 24 24 24 24 n
11 24 24 24 24 n
12 24 24 24 24 n
13 24 24 24 24 n
14 24 24 24 24 n
15 24 24 24 24 n
16 24 24 24 24 n
17 24 24 24 24 n
18 24 24 24 24 n
19 24 24 24 24 n
20 33 21 21 21 a
21 12 60 12 12 c
22 38 20 19 19 a
23 63 10 13 10 a
24 13 10 63 10 g
Binding TFs: 7khi_F (Sigma-70 factor, region 1.2, Sigma-70 factor, region 1.1, Sigma-70 region 3, Sigma-70 region 2 , Sigma-70, region 4, Sigma-70, non-essential region)
Binding Sites: 7khi_X
7khi_Y
Publications: Shin Y, Qayyum MZ, Pupov D, Esyunina D, Kulbachinskiy A, Murakami KS. Structural basis of ribosomal RNA transcription regulation. Nat Commun 12:528 (2021). [Pubmed]

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