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legend  pdf

structure nameTHE CRYO-EM STRUCTURE OF A BACTERIAL CLASS I TRANSCRIPTION ACTIVATION COMPLEX
(RNA POLYMERASE SIGMA FACTOR RPOD)
sourceESCHERICHIA COLI (STRAIN K12) / ESCHERICHIA COLI (STRAIN K12)
experimentNMR
structural superfamilySigma2 domain of RNA polymerase sigma factors;Sigma3 and sigma4 domains of RNA polymerase sigma factors;
sequence familySigma70, nonessential region; Sigma70 region 3; Sigma70 region 2; Sigma70, region 4; Sigma70 factor, region 12;
redundant complexes6ca0 4yln 4ylo 4ylp 3iyd
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureVRMRMLNRLNRFERYKSTYTWWQTRIVHENKEIDDLETERR

Estimated binding specificities ?

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# IC=21.147 IC/col=0.587 n_of_columns=36 specificity:   
A |   3  24  96   0   0  96   0   0  24   0  96   0  10  96   7  96  24  24  24  24  24  24  24  24  24  24  24  24  24  11   0   0  24  24   7   3
C |   3  24   0   0   0   0   0   0  24   0   0   0  72   0   7   0  24  24  24  24  24  24  24  24  24  24  24  24  24  11   0  96  24  24   7   3
G |  87  24   0  96  96   0   0   0  24   0   0  96   7   0   7   0  24  24  24  24  24  24  24  24  24  24  24  24  24  61   0   0  24  24  72  84
T |   3  24   0   0   0   0  96  96  24  96   0   0   7   0  75   0  24  24  24  24  24  24  24  24  24  24  24  24  24  13  96   0  24  24  10   6
scan!

Dendrogram of similar interfaces ?

matrix format
  
  VTRTMTRGMGLTNTRGLTNTRT----FAEARAYAKTSTTAYATAWTWT--QATARTITVTHTEGITNT----------------KTET------IGDG--DG----LTEGTT--ETRCRC------   L                    +-------------6b6h_F    
                                                                                                                                               +--------1 
  ------------NTRGLT--RC----FADAKAYA--SCTAYATCWTWT--QT------VTHTEA----RCRCEC------------EGIASAQAIC--EGDGSGFG----TTRGECRTRCQT----   L        +--2        +-------------6edt_F    
                                                                                                                                            !  ! 
  ------------NTRTLT----RTKTFAEARAFA--SATAYATAWTWTRA----------------------------------------------------------------------------   L     +--3  +----------------------3ugo_A    
                                                                                                                                         !  ! 
  ----------------------------------------------------------------------------------------------------------LTETTTRAECRCRCQC----   L   +-4  +-------------------------3n97_A    
                                                                                                                                       ! ! 
  ----------------------------------------------------------------------------------------------------------YG--------TGRGSGFTRG   L --5 +----------------------------2h27_A    
                                                                                                                                       ! 
  --------------------------------------------------------------------------NGRGTTRGKT------------------------------------------   L   +----------------------------5ds9_A    
                                                                                                                                     

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updated Mon Dec 18 14:29:31 2023