Structure of PDB 8to6 Chain L Binding Site BS01

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 O (length=56) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
caccgtgcgtgttgactattttacctctggcggtgataatggttgcatgt
actaag
Receptor-Ligand Complex Structure
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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)		V98 R99 M102 G106 L110 A382 R385 L386 K392 F419 E420 R423 Y425 K426 S428 T429 R451 P453 H455 T583 E585 R586
Binding residue
(residue number reindexed from 1)		V5 R6 M9 G13 L17 A240 R243 L244 K250 F277 E278 R281 Y283 K284 S286 T287 R309 P311 H313 T441 E443 R444
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

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

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