Structure of PDB 8to6 Chain L Binding Site BS02

Receptor Information
>8to6 Chain L (length=470) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITY
LLEQYDRVEAEEARLSDLITGFVDIDPELAREKFAELRAQYVVTRDTIKH
ATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCV
EQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ
KLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK
KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS
IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED
KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA
ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA
KALRKLRHPSRSEVLRSFLD
Ligand information
>8to6 Chain P (length=42) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cttagtacaccgccagaggtaaaatagtcaacacgcacggtg
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8to6 Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		W433 R562 L573 R584 R588
Binding residue
(residue number reindexed from 1)		W291 R420 L431 R442 R446
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0005515 protein binding
GO:0016987 sigma factor activity
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:0009408 response to heat
GO:0010468 regulation of gene expression
GO:0045892 negative regulation of DNA-templated transcription
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:1903865 sigma factor antagonist complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8to6, PDBe:8to6, PDBj:8to6
PDBsum8to6
PubMed38951624
UniProtP00579|RPOD_ECOLI RNA polymerase sigma factor RpoD (Gene Name=rpoD)

[Back to BioLiP]